Photochemical dynamics of laser-irradiated semiconductor nanostructures

Thesis (Ph.D.)--University of Washington, 2016-08

(Quantum-) critical dynamics of magnetoelectric materials

In this thesis the critical dynamics of several magnetoelectric compounds at their phase transition were examined. Mostly measurements of the dielectric properties in the frequency range of below 1 Hz up to 5 GHz were employed to evaluate the critical exponents for both magnetic field and temperature-dependent measurements. Most of the materials that are part of this work show anomalous behavior, especially at very low temperatures where quantum fluctuations are of the order of or even dominate those induced thermally. This anomalous behavior manifests in different forms. In Dy2Ti2O7 we demonstrate the existence of electric dipoles on magnetic monopoles. Here the dynamics at the critical endpoint located at 0.36K and in a magnetic field of 1T parallel to the [111] direction are of special interest. At this critical endpoint the expected critical slowing down of the dynamics could not only not be observed but instead the opposite, critical speeding-up by several orders of magnitude, could be demonstrated. Furthermore, we show that the phase diagram of Dy2Ti2O7 in this field direction can be reproduced solely from the dynamical properties, for example the resonance frequency of the observed relaxation that is connected to the monopole movement. Away from this point of the phase diagram the dynamics are slowing-down with reduction of temperature as one would expect. Additional measurements on Y2Ti2O7, a structurally identical but non-magnetic material, show only slowing down with reduction of temperature and no additional features. A possible explanation for the observed critical speeding-up is a coherent movement of magnetic monopoles close to the critical field that increases the resonance frequency by reducing the damping of the process. LiCuVO4 on the other hand behaves normally at its phase transition as long as the temperature is higher than 0.4 K. In this temperature regime the dynamics show critical slowing-down analogous to classical ferroelectric materials. This analogy extends also towards higher frequencies where the permittivity displays a ‘dispersion’ minimum that is temperature-dependent but of the order of 2 GHz. Below 0.4K the observed behavior changes drastically. Here we found no longer relaxational behavior but instead an excitation with very low energy. This low energy excitation was predicted by theory and is caused by nearly gapless soliton excitations within the 1D Cu2+ chains of LiCuVO4. Finally, in TbMnO3 the dynamics of the phase transition into the multiferroic phase was observed at roughly 27 K, a much higher temperature compared to the other materials. Here the expected critical slowing-down was observed, even though in low-frequency measurements this transition into the ferroelectric phase is overshadowed by the so-called c-axis relaxation. Therefore, only frequencies above 1MHz could be used to determine the critical exponents for both temperatureand magnetic-field-dependent measurements. This was done for both the peak frequency as well as the relaxation strength. In TbMnO3 an electromagnetic soft-mode with small optical weight causes the observed fluctuations, similar to the case of multiferroic MnWO4.

The shallow water approximation applied to the aluminium electrolysis process

The industrial production of aluminium is an electrolysis process where two superposed horizontal liquid layers are subjected to a mainly vertical electric current supplied by carbon electrodes. The lower layer consists of molten aluminium and lies on the cathode. The upper layer is the electrolyte and is covered by the anode. The interface between the two layers is often perturbed, leading to oscillations, or waves, similar to the waves on the surface of seas or lakes. The presence of electric currents and the resulting magnetic field are responsible for electromagnetic (Lorentz) forces within the fluid, which can amplify these oscillations and have an adverse influence on the process. The electrolytic bath vertical to horizontal aspect ratio is such, that it is advantageous to use the shallow water equations to model the interface motion. These are the depth-averaging the Navier-Stokes equations so that nonlinear and dispersion terms may be taken into account. Although these terms are essential to the prediction of wave dynamics, they are neglected in most of the literature on interface instabilities in aluminium reduction cells where only the linear theory is usually considered. The unknown variables are the two horizontal components of the fluid velocity, the height of the interface and the electric potential. In this application, a finite volume resolution of the double-layer shallow water equations including the electromagnetic sources has been developed, for incorporation into a generic three-dimensional computational fluid dynamics code that also deals with heat transfer within the cell.

Motivation in action: A process model of L2 motivation

As part of a long-term project aimed at designing classroom interventions to motivate language learners, we have searched for a motivation model that could serve as a theoretical basis for the methodological applications. We have found that none of the existing models we considered were entirely adequate for our purpose for three reasons: (1) they did not provide a sufficiently comprehensive and detailed summary of all the relevant motivational influences on classroom behaviour; (2) they tended to focus on how and why people choose certain courses of action, while ignoring or playing down the importance of motivational sources of executing goal-directed behaviour; and (3) they did not do justice to the fact that motivation is not static but dynamically evolving and changing in time, making it necessary for motivation constructs to contain a featured temporal axis. Consequently, partly inspired by Heckhausen and Kuhl's 'Action Control Theory', we have developed a new 'Process Model of L2 Motivation', which is intended both to account for the dynamics of motivational change in time and to synthesise many of the most important motivational conceptualisations to date. In this paper we describe the main components of this model, also listing a number of its limitations which need to be resolved in future research.

Analysis of Molecular Dynamics Simulations of Protein Folding

Microsecond long Molecular Dynamics (MD) trajectories of biomolecular processes are now possible due to advances in computer technology. Soon, trajectories long enough to probe dynamics over many milliseconds will become available. Since these timescales match the physiological timescales over which many small proteins fold, all atom MD simulations of protein folding are now becoming popular. To distill features of such large folding trajectories, we must develop methods that can both compress trajectory data to enable visualization, and that can yield themselves to further analysis, such as the finding of collective coordinates and reduction of the dynamics. Conventionally, clustering has been the most popular MD trajectory analysis technique, followed by principal component analysis (PCA). Simple clustering used in MD trajectory analysis suffers from various serious drawbacks, namely, (i) it is not data driven, (ii) it is unstable to noise and change in cutoff parameters, and (iii) since it does not take into account interrelationships amongst data points, the separation of data into clusters can often be artificial. Usually, partitions generated by clustering techniques are validated visually, but such validation is not possible for MD trajectories of protein folding, as the underlying structural transitions are not well understood. Rigorous cluster validation techniques may be adapted, but it is more crucial to reduce the dimensions in which MD trajectories reside, while still preserving their salient features. PCA has often been used for dimension reduction and while it is computationally inexpensive, being a linear method, it does not achieve good data compression. In this thesis, I propose a different method, a nonmetric multidimensional scaling (nMDS) technique, which achieves superior data compression by virtue of being nonlinear, and also provides a clear insight into the structural processes underlying MD trajectories. I illustrate the capabilities of nMDS by analyzing three complete villin headpiece folding and six norleucine mutant (NLE) folding trajectories simulated by Freddolino and Schulten [1]. Using these trajectories, I make comparisons between nMDS, PCA and clustering to demonstrate the superiority of nMDS. The three villin headpiece trajectories showed great structural heterogeneity. Apart from a few trivial features like early formation of secondary structure, no commonalities between trajectories were found. There were no units of residues or atoms found moving in concert across the trajectories. A flipping transition, corresponding to the flipping of helix 1 relative to the plane formed by helices 2 and 3 was observed towards the end of the folding process in all trajectories, when nearly all native contacts had been formed. However, the transition occurred through a different series of steps in all trajectories, indicating that it may not be a common transition in villin folding. The trajectories showed competition between local structure formation/hydrophobic collapse and global structure formation in all trajectories. Our analysis on the NLE trajectories confirms the notion that a tight hydrophobic core inhibits correct 3-D rearrangement. Only one of the six NLE trajectories folded, and it showed no flipping transition. All the other trajectories get trapped in hydrophobically collapsed states. The NLE residues were found to be buried deeply into the core, compared to the corresponding lysines in the villin headpiece, thereby making the core tighter and harder to undo for 3-D rearrangement. Our results suggest that the NLE may not be a fast folder as experiments suggest. The tightness of the hydrophobic core may be a very important factor in the folding of larger proteins. It is likely that chaperones like GroEL act to undo the tight hydrophobic core of proteins, after most secondary structure elements have been formed, so that global rearrangement is easier. I conclude by presenting facts about chaperone-protein complexes and propose further directions for the study of protein folding.

Coupling of Chemical Kinetics with Computational Fluid Dynamics in a Three-Dimensional Engine Model

The role of computer modeling has grown recently to integrate itself as an inseparable tool to experimental studies for the optimization of automotive engines and the development of future fuels. Traditionally, computer models rely on simplified global reaction steps to simulate the combustion and pollutant formation inside the internal combustion engine. With the current interest in advanced combustion modes and injection strategies, this approach depends on arbitrary adjustment of model parameters that could reduce credibility of the predictions. The purpose of this study is to enhance the combustion model of KIVA, a computational fluid dynamics code, by coupling its fluid mechanics solution with detailed kinetic reactions solved by the chemistry solver, CHEMKIN. As a result, an engine-friendly reaction mechanism for n-heptane was selected to simulate diesel oxidation. Each cell in the computational domain is considered as a perfectly-stirred reactor which undergoes adiabatic constant- volume combustion. The model was applied to an ideally-prepared homogeneous- charge compression-ignition combustion (HCCI) and direct injection (DI) diesel combustion. Ignition and combustion results show that the code successfully simulates the premixed HCCI scenario when compared to traditional combustion models. Direct injection cases, on the other hand, do not offer a reliable prediction mainly due to the lack of turbulent-mixing model, inherent in the perfectly-stirred reactor formulation. In addition, the model is sensitive to intake conditions and experimental uncertainties which require implementation of enhanced predictive tools. It is recommended that future improvements consider turbulent-mixing effects as well as optimization techniques to accurately simulate actual in-cylinder process with reduced computational cost. Furthermore, the model requires the extension of existing fuel oxidation mechanisms to include pollutant formation kinetics for emission control studies.

Tourism Media Dynamics: Narratives of the Nation-State

With the premise that the tourism promotional video “China, Forever” provides a crucial access to understanding how tourism engages in a wider circle of socio-culture formation, this dissertation research approaches tourism by examining communicative practices initiated by “China, Forever”. In doing so, it seeks to reveal two dialogues – firstly, between the discursive construction of tourism representational language and China’s nation-state ideology; secondly, between interpretations from overseas Chinese audiences and nation-state narratives delivered via the tourism media. In analyzing the first dialogue, this dissertation reveals that the pursuit of collective and monolithic national imagery has caused a representational violence – one that is committed by the nation-state ideology operated through the organization of tourism language. The very representational coercion itself, however, signifies the nature of tourism media as a vehicle mediating the global gaze and China’s self-representation; illuminating the fact that China’s nation-state building is only to be understood as deeply-grounded in the complexity of postcolonial politics. Furthermore, in a dialectic view, such finding consolidates the nature of “China, Forever” as a cultural product that actively exists as a component in the overall social fabric, co-creating a wider circle of culture politics together with other genres of media products; thus, calling for a more comprehensive understanding of tourism media at large. In the second approach, this dissertation seeks to understand how the tourism video “China, Forever” mediates the relationship between tourism narratives of the nation-state and overseas Chinese individuals; thus bridging together tourism media and ongoing life experiences of the audiences chosen. The analysis reveals that audiences’ interpretations heavily concentrate on resisting and fragmenting the hegemonic nation-state language in “China, Forever”. While some interviewees seek to decentralize the nation-state perspective from aspects of aesthetics, representational style, and representational subjects in “China, Forever” by incorporating their individual memories and past experiences, to some others, the over-polished glorification of China in the mediated tourism discourse is only coercive to China’s social realities experienced by the individual interviewees - the disheartening contrasts of poverty and affluence as well as other social inequalities. From the perspective of the audience group, the Chinese scholars and students at the University of Illinois interviewed for this dissertation research constitute a cohort of exiled audiences for the tourism video “China, Forever”. The audiences subject themselves to voluntary interpellation, a process in which they find themselves defending, negotiating, and resisting the nation-state representation of China – even though they are not its intended audience and have had no input into its production. Nevertheless, such process is one of identification, in which viewers articulate a subject position from which to speak of their own experiences, dilemmas and desires. The usefulness of tourism media discourse in mediating the nation-state narratives and the individual experience is amplified.

The Political and Social Dynamics of Poverty, Poor Relief and Health Care in Early-Modern Portugal

By the end of the fifteenth century most European countries had witnessed a profound reformation of their poor relief and health care policies. As this book demonstrates, Portugal was among them and actively participated in such reforms. Providing the first English language monograph on this topic, Laurinda Abreu examines the Portuguese experience and places it within the broader European context. She shows that, in line with much that was happening throughout the rest of Europe, Portugal had not only set up a systematic reform of the hospitals but had also developed new formal arrangements for charitable and welfare provision that responded to the changing socioeconomic framework, the nature of poverty and the concerns of political powers. The defining element of the Portuguese experience was the dominant role played by a new lay confraternity, the confraternity of the Misericórdia, created under the auspices of King D. Manuel I in 1498. By the time of the king's death in 1521 there were more than 70 Misericórdias in Portugal and its empire, and by 1640, more than 300. All of them were run according to a unified set of rules and principles with identical social objectives. Based upon a wealth of primary source documentation, this book reveals how the sixteenth-century Portuguese crown succeeded in implementing a national poor relief and health care structure, with the support of the Papacy and local elites, and funded principally through pious donations. This process strengthened the authority of the royal government at a time which coincided with the emergence of the early modern state. In so doing, the book establishes poor relief and public health alongside military, diplomatic and administrative authorities, as the pillars of centralisation of royal power.

Shape and chemically anisotropic colloidal particles: A theoretical study of their structure, phase behavior, and slow dynamics

A detailed non-equilibrium state diagram of shape-anisotropic particle fluids is constructed. The effects of particle shape are explored using Naive Mode Coupling Theory (NMCT), and a single particle Non-linear Langevin Equation (NLE) theory. The dynamical behavior of non-ergodic fluids are discussed. We employ a rotationally frozen approach to NMCT in order to determine a transition to center of mass (translational) localization. Both ideal and kinetic glass transitions are found to be highly shape dependent, and uniformly increase with particle dimensionality. The glass transition volume fraction of quasi 1- and 2- dimensional particles fall monotonically with the number of sites (aspect ratio), while 3-dimensional particles display a non-monotonic dependence of glassy vitrification on the number of sites. Introducing interparticle attractions results in a far more complex state diagram. The ideal non-ergodic boundary shows a glass-fluid-gel re-entrance previously predicted for spherical particle fluids. The non-ergodic region of the state diagram presents qualitatively different dynamics in different regimes. They are qualified by the different behaviors of the NLE dynamic free energy. The caging dominated, repulsive glass regime is characterized by long localization lengths and barrier locations, dictated by repulsive hard core interactions, while the bonding dominated gel region has short localization lengths (commensurate with the attraction range), and barrier locations. There exists a small region of the state diagram which is qualified by both glassy and gel localization lengths in the dynamic free energy. A much larger (high volume fraction, and high attraction strength) region of phase space is characterized by short gel-like localization lengths, and long barrier locations. The region is called the attractive glass and represents a 2-step relaxation process whereby a particle first breaks attractive physical bonds, and then escapes its topological cage. The dynamic fragility of fluids are highly particle shape dependent. It increases with particle dimensionality and falls with aspect ratio for quasi 1- and 2- dimentional particles. An ultralocal limit analysis of the NLE theory predicts universalities in the behavior of relaxation times, and elastic moduli. The equlibrium phase diagram of chemically anisotropic Janus spheres and Janus rods are calculated employing a mean field Random Phase Approximation. The calculations for Janus rods are corroborated by the full liquid state Reference Interaction Site Model theory. The Janus particles consist of attractive and repulsive regions. Both rods and spheres display rich phase behavior. The phase diagrams of these systems display fluid, macrophase separated, attraction driven microphase separated, repulsion driven microphase separated and crystalline regimes. Macrophase separation is predicted in highly attractive low volume fraction systems. Attraction driven microphase separation is charaterized by long length scale divergences, where the ordering length scale determines the microphase ordered structures. The ordering length scale of repulsion driven microphase separation is determined by the repulsive range. At the high volume fractions, particles forgo the enthalpic considerations of attractions and repulsions to satisfy hard core constraints and maximize vibrational entropy. This results in site length scale ordering in rods, and the sphere length scale ordering in Janus spheres, i.e., crystallization. A change in the Janus balance of both rods and spheres results in quantitative changes in spinodal temperatures and the position of phase boundaries. However, a change in the block sequence of Janus rods causes qualitative changes in the type of microphase ordered state, and induces prominent features (such as the Lifshitz point) in the phase diagrams of these systems. A detailed study of the number of nearest neighbors in Janus rod systems reflect a deep connection between this local measure of structure, and the structure factor which represents the most global measure of order.

Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface

The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants hCx46N188Q and hCx46N188D. Within the 50 ns simulation time the docked complex composed of the mutants dissociate while hCx46wt remains stable. The data indicates that one hCx46 molecule forms 5-7 hydrogen bonds (HBs) with the counterpart connexin of the opposing connexon. These HBs appear essential for a stable docking of the connexons as shown by the simulation of an entire gap junction channel and were lost for all the tested mutants. The data described here are related to the research article entitled "The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels" (Schadzek et al., 2015) [1].

Predictive Models for Tomato Spotted Wilt Virus Spread Dynamics, Considering Frankliniella occidentalis Specific Life Processes as Influenced by the Virus

Several models have been studied on predictive epidemics of arthropod vectored plant viruses in an attempt to bring understanding to the complex but specific relationship between the three cornered pathosystem (virus, vector and host plant), as well as their interactions with the environment. A large body of studies mainly focuses on weather based models as management tool for monitoring pests and diseases, with very few incorporating the contribution of vector's life processes in the disease dynamics, which is an essential aspect when mitigating virus incidences in a crop stand. In this study, we hypothesized that the multiplication and spread of tomato spotted wilt virus (TSWV) in a crop stand is strongly related to its influences on Frankliniella occidentalis preferential behavior and life expectancy. Model dynamics of important aspects in disease development within TSWV-F. occidentalis-host plant interactions were developed, focusing on F. occidentalis' life processes as influenced by TSWV. The results show that the influence of TSWV on F. occidentalis preferential behaviour leads to an estimated increase in relative acquisition rate of the virus, and up to 33% increase in transmission rate to healthy plants. Also, increased life expectancy; which relates to improved fitness, is dependent on the virus induced preferential behaviour, consequently promoting multiplication and spread of the virus in a crop stand. The development of vector-based models could further help in elucidating the role of tri-trophic interactions in agricultural disease systems. Use of the model to examine the components of the disease process could also boost our understanding on how specific epidemiological characteristics interact to cause diseases in crops. With this level of understanding we can efficiently develop more precise control strategies for the virus and the vector.

Frequency of elemental events of intracellular Ca²⁺ dynamics

The dynamics of intracellular Ca²⁺ is driven by random events called Ca²⁺ puffs, in which Ca²⁺ is liberated from intracellular stores. We show that the emergence of Ca²⁺ puffs can be mapped to an escape process. The mean first passage times that correspond to the stochastic fraction of puff periods are computed from a novel master equation and two Fokker-Planck equations. Our results demonstrate that the mathematical modeling of Ca²⁺ puffs has to account for the discrete character of the Ca²⁺ release sites and does not permit a continuous description of the number of open channels.

Influences of change strategies to achieve organizational flexibility: a system dynamics approach.

257 p.

Minerals and vitamin B9 in dried plants vs. infusions: assessing absorption dynamics of minerals by membrane dialysis tandem in vitro digestion

Vitamins and mineral elements are among the most important phytochemicals due to their important role in the maintenance of human health. Despite these components had already been studied in different plant species, their full characterization in several wild species is still scarce. In addition, the knowledge regarding the in vivo effects of phytochemicals, particularly their bioaccessibility, is still scarce. Accordingly, a membrane dialysis process was used to simulate gastrointestinal conditions in order to assess the potential bioaccessibility of mineral elements in different preparations of Achillea millefolium (yarrow), Laurus nobilis (laurel) and Taraxacum sect. Ruderalia (dandelion). The retention/passage dynamics was evaluated using a cellulose membrane with 34 mm pore. Dandelion showed the highest levels of all studied mineral elements (except zinc) independently of the used formulations (dried plant or infusion), but yarrow was the only species yielding minerals after the dialysis step, either in dried form, or as infusion. In fact, the ability of each evaluated element to cross the dialysis membrane showed significant differences, being also highly dependent on the plant species. Regarding the potential use of these plants as complementary vitamin B9 sources, the detected values were much lower in the infusions, most likely due to the thermolability effect.

PHYSICAL FACTORS IN B CELL ACTIN DYNAMICS AND ACTIVATION

Cells adapt to their changing world by sensing environmental cues and responding appropriately. This is made possible by complex cascades of biochemical signals that originate at the cell membrane. In the last decade it has become apparent that the origin of these signals can also arise from physical cues in the environment. Our motivation is to investigate the role of physical factors in the cellular response of the B lymphocyte. B cells patrol the body for signs of invading pathogens in the form of antigen on the surface of antigen presenting cells. Binding of antigen with surface proteins initiates biochemical signaling essential to the immune response. Once contact is made, the B cell spreads on the surface of the antigen presenting cell in order to gather as much antigen as possible. The physical mechanisms that govern this process are unexplored. In this research, we examine the role of the physical parameters of antigen mobility and cell surface topography on B cell spreading and activation. Both physical parameters are biologically relevant as immunogens for vaccine design, which can provide laterally mobile and immobile antigens and topographical surfaces. Another physical parameter that influences B cell response and the formation of the cell-cell junction is surface topography. This is biologically relevant as antigen presenting cells have highly convoluted membranes, resulting in variable topography. We found that B cell activation required the formation of antigen-receptor clusters and their translocation within the attachment plane. We showed that cells which failed to achieve these mobile clusters due to prohibited ligand mobility were much less activation competent. To investigate the effect of topography, we use nano- and micro-patterned substrates, on which B cells were allowed to spread and become activated. We found that B cell spreading, actin dynamics, B cell receptor distribution and calcium signaling are dependent on the topographical patterning of the substrate. A quantitative understanding of cellular response to physical parameters is essential to uncover the fundamental mechanisms that drive B cell activation. The results of this research are highly applicable to the field of vaccine development and therapies for autoimmune diseases. Our studies of the physical aspects of lymphocyte activation will reveal the role these factors play in immunity, thus enabling their optimization for biological function and potentially enabling the production of more effective vaccines.