Molecular dynamics simulations of sheared brush-like systems

Mit Hilfe von Molekulardynamik-Simulationen untersuchen wir bürstenartige Systeme unter guten Lösungsmittelbedingungen. Diese Systeme sind, dank ihren vielfältigen Beschaffenheiten, die von Molekularparametern und äußeren Bedingungen abhängig sind, wichtig für viele industrielle Anwendungen. Man vermutet, dass die Polymerbürsten eine entscheidende Rolle in der Natur wegen ihrer einzigartigen Gleiteigenschaften spielen. Ein vergröbertes Modell wird verwendet, um die strukturellen und dynamischen Eigenschaften zweier hochkomprimierter Polymerbürsten, die eine niedrige Reibung aufweisen, zu untersuchen. Allerdings sind die Lubrikationseigenschaften dieser Systeme, die in vielen biologischen Systemen vorhanden sind, beeinflußt. Wir untersuchen so-genannte "weiche Kolloide", die zwischen den beiden Polymerbürsten eingebettet sind, und wie diese Makroobjekte auf die Polymerbürsten wirken.rnrnNicht-Gleichgewichts-Molekulardynamik-Simulationen werden durchgeführt, in denen die hydrodynamischen Wechselwirkungen durch die Anwendung des DPD-Thermostaten mit expliziten Lösungsmittelmolekülen berücksichtigt werden. Wir zeigen, dass die Kenntnis der Gleichgewichtseigenschaften des Systems erlaubt, dynamische Nichtgleichgewichtsigenschaften der Doppelschicht vorherzusagen.rnrnWir untersuchen, wie die effektive Wechselwirkung zwischen kolloidalen Einschlüßen durch die Anwesenheit der Bürsten (in Abhängigkeit der Weichheit der Kolloide und der Pfropfdichte der Bürsten) beeinflußt wird. Als nächsten Schritt untersuchen wir die rheologische Antwort von solchen komplexen Doppelschichten auf Scherung. Wir entwickeln eine Skalen-Theorie, die die Abhängigkeit der makroskopischen Transporteigenschaften und der lateralen Ausdehnung der verankerten Ketten von der Weissenberg Zahl oberhalb des Bereichs, in dem die lineare Antwort-Theorie gilt, voraussagt. Die Vorhersagen der Theorie stimmen gut mit unseren und früheren numerischen Ergebnissen und neuen Experimenten überein. Unsere Theorie bietet die Möglichkeit, die Relaxationszeit der Doppelschicht zu berechnen. Wenn diese Zeit mit einer charakteristischen Längenskala kombiniert wird, kann auch das ''transiente'' (nicht-stationäre) Verhalten beschrieben werden.rnrnrnWir untersuchen die Antwort des Drucktensors und die Deformation der Bürsten während der Scherinvertierung für grosse Weissenberg Zahlen. Wir entwickeln eine Vorhersage für die charakteristische Zeit, nach der das System wieder den stationären Zustand erreicht.rnrnrnElektrostatik spielt eine bedeutende Rolle in vielen biologischen Prozessen. Die Lubrikationseigenschaften der Polymerbürsten werden durch die Anwesenheit langreichweitiger Wechselwirkungen stark beeinflusst. Für unterschiedliche Stärken der elektrostatischen Wechselwirkungen untersuchen wir rheologische Eigenschaften der Doppelschicht und vergleichen mit neutralen Systemen. Wir studieren den kontinuierlichen Übergang der Systemeigenschaften von neutralen zu stark geladenen Bürsten durch Variation der Bjerrumlänge und der Ladungsdichte.

Novel investigation methods in Computational Social Dynamics and Complex Systems

In this thesis the evolution of the techno-social systems analysis methods will be reported, through the explanation of the various research experience directly faced. The first case presented is a research based on data mining of a dataset of words association named Human Brain Cloud: validation will be faced and, also through a non-trivial modeling, a better understanding of language properties will be presented. Then, a real complex system experiment will be introduced: the WideNoise experiment in the context of the EveryAware european project. The project and the experiment course will be illustrated and data analysis will be displayed. Then the Experimental Tribe platform for social computation will be introduced . It has been conceived to help researchers in the implementation of web experiments, and aims also to catalyze the cumulative growth of experimental methodologies and the standardization of tools cited above. In the last part, three other research experience which already took place on the Experimental Tribe platform will be discussed in detail, from the design of the experiment to the analysis of the results and, eventually, to the modeling of the systems involved. The experiments are: CityRace, about the measurement of human traffic-facing strategies; laPENSOcosì, aiming to unveil the political opinion structure; AirProbe, implemented again in the EveryAware project framework, which consisted in monitoring air quality opinion shift of a community informed about local air pollution. At the end, the evolution of the technosocial systems investigation methods shall emerge together with the opportunities and the threats offered by this new scientific path.

Excited-state dynamics in donor-acceptor systems for energy conversion

In dieser Arbeit werden die Dynamiken angeregter Zustände in Donor-Akzeptorsystemen für Energieumwandlungsprozesse mit ultraschneller zeitaufgelöster optischer Spektroskopie behandelt. Der Hauptteil dieser Arbeit legt den Fokus auf die Erforschung der Photophysik organischer Solarzellen, deren aktive Schichten aus diketopyrrolopyrrole (DPP) basierten Polymeren mit kleiner Bandlücke als Elektronendonatoren und Fullerenen als Elektronenakzeptoren bestehen. rnEin zweiter Teil widmet sich der Erforschung von künstlichen primären Photosynthesereaktionszentren, basierend auf Porphyrinen, Quinonen und Ferrocenen, die jeweils als Lichtsammeleinheit, Elektronenakzeptor beziehungsweise als Elektronendonatoren eingesetzt werden, um langlebige ladungsgetrennte Zustände zu erzeugen.rnrnZeitaufgelöste Photolumineszenzspektroskopie und transiente Absorptionsspektroskopie haben gezeigt, dass Singulettexzitonenlebenszeiten in den Polymeren PTDPP-TT und PFDPP-TT Polymeren kurz sind (< 20 ps) und dass in Mischungen der Polymere mit PC71BM geminale Rekombination von gebundenen Ladungstransferzuständen ein Hauptverlustkanal ist. Zudem wurde in beiden Systemen schnelle nichtgeminale Rekombination freier Ladungen zu Triplettzuständen auf dem Polymer beobachtet. Für das Donor-Akzeptor System PDPP5T:PC71BM wurde nachgewiesen, dass die Zugabe eines Lösungsmittels mit hohem Siedepunkt, und zwar ortho-Dichlorbenzol, die Morphologie der aktiven Schicht stark beeinflusst und die Solarzelleneffizienz verbessert. Der Grund hierfür ist, dass die Donator- und Akzeptormaterialien besser durchmischt sind und sich Perkolationswege zu den Elektroden ausgebildet haben, was zu einer verbesserten Ladungsträgergeneration und Extraktion führt. Schnelle Bildung des Triplettzustands wurde in beiden PDPP5T:PC71BM Systemen beobachtet, da der Triplettzustand des Polymers über Laungstransferzustände mit Triplettcharakter populiert werden kann. "Multivariate curve resolution" (MCR) Analyse hat eine starke Intensitätsabhängigkeit gezeigt, was auf nichtgeminale Ladungsträgerrekombination in den Triplettzustand hinweist.rnrnIn den künstlichen primären Photosynthesereaktionszentren hat transiente Absorptionsspektroskopie bestätigt, dass photoinduzierter Ladungstransfer in Quinon-Porphyrin (Q-P) und Porphyrin-Ferrocen (P-Fc) Diaden sowie in Quinon-Porphyrin-Ferrocen (Q-P-Fc) Triaden effizient ist. Es wurde jedoch auch gezeigt, dass in den P-Fc unf Q-P-Fc Systemen die ladungsgetrennten Zustände in den Triplettzustand der jeweiligen Porphyrine rekombinieren. Der ladungsgetrennte Zustand konnte in der Q-P Diade durch Zugabe einer Lewissäure signifikant stabilisiert werden.

Uncovering the dynamics of cardiac systems using stochastic pacing and frequency domain analyses

Alternans of cardiac action potential duration (APD) is a well-known arrhythmogenic mechanism which results from dynamical instabilities. The propensity to alternans is classically investigated by examining APD restitution and by deriving APD restitution slopes as predictive markers. However, experiments have shown that such markers are not always accurate for the prediction of alternans. Using a mathematical ventricular cell model known to exhibit unstable dynamics of both membrane potential and Ca2+ cycling, we demonstrate that an accurate marker can be obtained by pacing at cycle lengths (CLs) varying randomly around a basic CL (BCL) and by evaluating the transfer function between the time series of CLs and APDs using an autoregressive-moving-average (ARMA) model. The first pole of this transfer function corresponds to the eigenvalue (λalt) of the dominant eigenmode of the cardiac system, which predicts that alternans occurs when λalt≤−1. For different BCLs, control values of λalt were obtained using eigenmode analysis and compared to the first pole of the transfer function estimated using ARMA model fitting in simulations of random pacing protocols. In all versions of the cell model, this pole provided an accurate estimation of λalt. Furthermore, during slow ramp decreases of BCL or simulated drug application, this approach predicted the onset of alternans by extrapolating the time course of the estimated λalt. In conclusion, stochastic pacing and ARMA model identification represents a novel approach to predict alternans without making any assumptions about its ionic mechanisms. It should therefore be applicable experimentally for any type of myocardial cell.

Real-time dynamics of open quantum spin systems driven by dissipative processes

We study the real-time evolution of large open quantum spin systems in two spatial dimensions, whose dynamics is entirely driven by a dissipative coupling to the environment. We consider different dissipative processes and investigate the real-time evolution from an ordered phase of the Heisenberg or XY model towards a disordered phase at late times, disregarding unitary Hamiltonian dynamics. The corresponding Kossakowski-Lindblad equation is solved via an efficient cluster algorithm. We find that the symmetry of the dissipative process determines the time scales, which govern the approach towards a new equilibrium phase at late times. Most notably, we find a slow equilibration if the dissipative process conserves any of the magnetization Fourier modes. In these cases, the dynamics can be interpreted as a diffusion process of the conserved quantity.

Dynamics in the governance of collective irrigation systems: Evidence from field experiments in Nicaragua.

In this paper, we investigate the real demand for climate protection when the purely individual perspective of existing revealed preference studies is relaxed. This is achieved in two treatments; first, we determine the information subjects receive about the demand revealed by other subjects in a similar decision making situation, second, collective action is implemented whereby all subjects are required to purchase the group?s median quantity at a given price. Participants in the experiment were offered the opportunity to contribute to climate protection by purchasing European Union Allowances. Allowances purchased were withdrawn from the European Emissions Trading Scheme. In our experiment, information about other subjects? behaviour has no treatment effect on the demand for climate protection. Under collective action however, the probability of purchasing allowances is higher compared to the reference treatment situation, an individual contribution mechanism. Furthermore, we observe a strong correlation between subjects? demand and their expectations about other participants? behaviour. When collective action is not available, subjects? e xpectations are consistent with free rider behaviour.

Dynamics in the governance of collective irrigation systems: Evidence from field experiments in Nicaragua.

The objective of this study is to analyze the common pool resource appropriation and public good provisiondecisions in a dynamic setting, testing the differences in behavior and performance between lab and field subjects. We performeda total of 45 games in Nicaragua, including 88 villagers in rural communities and 92 undergraduate students. In order to analyze sequential decision making, we introduce a dynamic and asymmetric irrigation game that combines the typical social dilemmas associated to irrigation systems management.In addition, in 9 out of 22 villagers’ groups, we implemented a treatment that included the disclosure of subjects’ appropriation of the common pool resource. The results reveal that the provision of individuals’ appropriation level results in higher appropriation in subsequent rounds. In addition, the results show that non-treated villagers provide more public good than treated villagers but if compared with students the differences are not significant. The results also suggest that appropriation levels are below the Nash prediction of full appropriation, but above the social efficient level. This results in an efficiency loss in the game that can be explained to a large extent by individual decisions on appropriation and public good contribution and by group appropriation behavior.

On the application of meshfree methods to the nonlinear dynamics of multibody systems

Esta tesis propone una completa formulación termo-mecánica para la simulación no-lineal de mecanismos flexibles basada en métodos libres de malla. El enfoque se basa en tres pilares principales: la formulación de Lagrangiano total para medios continuos, la discretización de Bubnov-Galerkin, y las funciones de forma libres de malla. Los métodos sin malla se caracterizan por la definición de un conjunto de funciones de forma en dominios solapados, junto con una malla de integración de las ecuaciones discretas de balance. Dos tipos de funciones de forma se han seleccionado como representación de las familias interpolantes (Funciones de Base Radial) y aproximantes (Mínimos Cuadrados Móviles). Su formulación se ha adaptado haciendo sus parámetros compatibles, y su ausencia de conectividad predefinida se ha aprovechado para interconectar múltiples dominios de manera automática, permitiendo el uso de mallas de fondo no conformes. Se propone una formulación generalizada de restricciones, juntas y contactos, válida para sólidos rígidos y flexibles, siendo estos últimos discretizados mediante elementos finitos (MEF) o libres de malla. La mayor ventaja de este enfoque reside en que independiza completamente el dominio con respecto de las uniones y acciones externas a cada sólido, permitiendo su definición incluso fuera del contorno. Al mismo tiempo, también se minimiza el número de ecuaciones de restricción necesarias para la definición de uniones realistas. Las diversas validaciones, ejemplos y comparaciones detalladas muestran como el enfoque propuesto es genérico y extensible a un gran número de sistemas. En concreto, las comparaciones con el MEF indican una importante reducción del error para igual número de nodos, tanto en simulaciones mecánicas, como térmicas y termo-mecánicas acopladas. A igualdad de error, la eficiencia numérica de los métodos libres de malla es mayor que la del MEF cuanto más grosera es la discretización. Finalmente, la formulación se aplica a un problema de diseño real sobre el mantenimiento de estructuras masivas en el interior de un reactor de fusión, demostrando su viabilidad en análisis de problemas reales, y a su vez mostrando su potencial para su uso en simulación en tiempo real de sistemas no-lineales. A new complete formulation is proposed for the simulation of nonlinear dynamic of multibody systems with thermo-mechanical behaviour. The approach is founded in three main pillars: total Lagrangian formulation, Bubnov-Galerkin discretization, and meshfree shape functions. Meshfree methods are characterized by the definition of a set of shape functions in overlapping domains, and a background grid for integration of the Galerkin discrete equations. Two different types of shape functions have been chosen as representatives of interpolation (Radial Basis Functions), and approximation (Moving Least Squares) families. Their formulation has been adapted to use compatible parameters, and their lack of predefined connectivity is used to interconnect different domains seamlessly, allowing the use of non-conforming meshes. A generalized formulation for constraints, joints, and contacts is proposed, which is valid for rigid and flexible solids, being the later discretized using either finite elements (FEM) or meshfree methods. The greatest advantage of this approach is that makes the domain completely independent of the external links and actions, allowing to even define them outside of the boundary. At the same time, the number of constraint equations needed for defining realistic joints is minimized. Validation, examples, and benchmarks are provided for the proposed formulation, demonstrating that the approach is generic and extensible to further problems. Comparisons with FEM show a much lower error for the same number of nodes, both for mechanical and thermal analyses. The numerical efficiency is also better when coarse discretizations are used. A final demonstration to a real problem for handling massive structures inside of a fusion reactor is presented. It demonstrates that the application of meshfree methods is feasible and can provide an advantage towards the definition of nonlinear real-time simulation models.

Symmetry, stability, and dynamics of multidomain and multicomponent protein systems

Symmetry is commonly observed in many biological systems. Here we discuss representative examples of the role of symmetry in structural molecular biology. Point group symmetries are observed in many protein oligomers whose three-dimensional atomic structures have been elucidated by x-ray crystallography. Approximate symmetry also occurs in multidomain proteins. Symmetry often confers stability on the molecular system and results in economical usage of basic components to build the macromolecular structure. Symmetry is also associated with cooperativity. Mild perturbation from perfect symmetry may be essential in some systems for dynamic functions.

Complex dynamics of multilocus systems subjected to cyclical selection.

Earlier we have shown that oscillations with a long period ("supercycles") may arise in two-locus systems experiencing cyclical selection with a short period. However, this mode of complex limiting behavior appeared to be possible for narrow ranges of parameters. Here we demonstrate that a multilocus system subjected to stabilizing selection with cyclically moving optimum can generate ubiquitous complex limiting behavior including supercycles, T-cycles, and chaotic-like phenomena. This mode of multilocus dynamics far exceeds the potential attainable under ordinary selection models resulting in simple behavior. It may represent a novel evolutionary mechanism increasing genetic diversity over long-term time periods.

Hearings on the Navy proposal to modify SSN-688 contracts with the General Dynamics Corp. (Electric Boat Division) and LHA and DD-963 contracts with Litton Industries, Inc./Litton Systems, Inc. (Ingalls Shipbuilding Division /

Mode of access: Internet.

Dynamics of loads on power systems using field measurements /

"May 1984."

Facilitating Realistic and Efficient Applications of Ab Initio Electronic Dynamics for Polyatomic Systems

Thesis (Ph.D.)--University of Washington, 2016-06