Abstract not available

Thesis (M.S.)--Oregon State University, 2008. / Printout. Includes bibliographical references (leaves 107-117). Also available on the World Wide Web.

This thesis consists of four research papers. In the first paper we construct nonmetrizable compact convex sets with pathological sets of simpliciality, show- ing that the properties of the set of simpliciality known in the metrizable case do not hold without the assumption of metrizability. In the second paper we construct an example concerning remotal sets, answering thus a question of Martín and Rao, and present a new proof of the fact that in every infinite- dimensional Banach space there exists a closed convex bounded set which is not remotal. The third paper is a study of the relations between polynomials on Banach spaces and linear identities. We investigate under which conditions a linear identity is satisfied only by polynomials, and describe the space of poly- nomials satisfying such linear identity. In the last paper we study the coarse and uniform embeddability between Orlicz sequence spaces. We show that the embeddability between two Orlicz sequence spaces is in most cases determined only by the values of their upper Matuszewska-Orlicz indices. 1

En la actualidad en gran parte del mundo se viene proponiendo e impulsando las políticas ambientales que puedan reducir el problema de la degradación de los recursos naturales a la que está siendo sometido el planeta. A tal efecto se plantea la realización de esta investigación para tratar de determinar el grado de influencia en las propiedades físicas del concreto fabricado con agregados reciclados procedentes de la trituración. La variable seleccionada para la investigación ha sido: el porcentaje de sustitución del agregado grueso natural por agregado grueso reciclado en la dosificación del concreto. El objetivo general de la investigación es analizar en qué medida la cantidad de agregado grueso reciclado usado en la dosificación de la mezcla influye en las propiedades mecánicas del concreto. El tipo de investigación fue básica y cualitativa, la metodología. Se usó una metodología experimental y transversal. El análisis de los resultados experimentales indican que la resistencia a la compresión y a la tracción no se ven afectadas notoriamente al reemplazar el 20% de agregado natural, en un mayor porcentaje de reemplazo , la resistencia empieza a decaer directamente proporcional a un mayor porcentaje de agregado reciclado. Today in much of the world has been proposing and promoting environmental policies that can reduce the problem of the degradation of natural resources that the planet is undergoing. For this purpose the realization of this research to try to determine the degree of influence on the physical properties of concrete made with recycled aggregate from crushing arises. The selected research variable was the percentage of coarse natural aggregate replacement by recycled coarse aggregate concrete proportions. The overall objective of the research is to analyze to what extent the amount of recycled coarse aggregate used in the dosage of the mixture influences the mechanical properties of concrete. The research was basic and qualitative methodology. An experimental and transversal approach was used. Analysis of the experimental results indicate that the compressive strength and tensile strength are not affected noticeably by replacing 20% of natural aggregate, a higher percentage replacement, resistance begins to drop directly proportional to a higher percentage of added recycling.

Le modèle de Poland-Scheraga (PS) est le modèle standard pour étudier la transition de dénaturation de deux brins d’ADN complémentaires et de même longueur. Ce modèle a fait l’objet d’une attention remarquable car il est exactement résoluble dans sa version homogène. Le caractère résoluble est lié au fait que le modèle PS homogène peut être mis en correspondance avec un processus de renouvellement discret. Dans la littérature biophysique une généralisation du modèle, obtenue en considérant des brins non complé- mentaires et de longueurs différentes, a été considérée et le caractère résoluble s’étend à cette généralisation substantielle. Dans cette thèse, nous présentons une analyse mathématique du modèle de Poland- Scheraga généralisé. Nous considérons d’abord le modèle homogène et nous exploitons que les deux brins de la chaîne peuvent être modélisés par un processus de renouvellement en deux dimensions. La distribution K(⋅) de l’emplacement (bidimensionnel) du premier contact entre les deux brins est supposée de la forme K(n+m) = (n+m)−α−2L(n+m) avec α ≥ 0 et L(⋅) à variation lente et correspond à une boucle avec n bases dans le premier brin et m dans le deuxième. Nous étudions la transition de localisation-délocalisation et nous montrons l’existence des transitions à l’intérieur de la phase localisée. Nous présentons ensuite des estimations précises sur les propriétés de chemin du modèle. Ensuite, nous étudions la version désordonnée du modèle en incluant une séquence de variables aléatoires indépendantes identiquement distribuées à deux indices. Nous nous concentrons sur l’influence du désordre sur la transition de dénaturation: nous voulons déterminer si la présence des inhomogénéités modifie les propriétés critiques du système par rapport au cas homogène. Nous prouvons que le désordre est non pertinent si α < 1 et nous montrons que pour α > 1, les points critiques gelés et recuits diffèrent (basant sur les techniques de coarse graining et la méthode des moments fractionnaires), ce qui prouve la présence d’un régime de désordre pertinent. / The Poland-Scheraga (PS) model is the standard basic model to study the denaturation transition of two complementary and equally long strands of DNA. This model has enjoyed a remarkable attention because it is exactly solvable in its homogeneous version. The solvable character is related to the fact that the homogeneous PS model can be mapped to a discrete renewal process. In the bio-physical literature a generalization of the model, allowing different length and non complementarity of the strands, has been considered and the solvable character extends to this substantial generalization. In this thesis we present a generalized version of the PS model that allows mismatches and non complementary strands (in particular, the two strands may be of different lengths). We consider first the homogeneous model and we exploit that this model can be mapped to a bivariate renewal process. The distribution K(⋅) of the location (in two dimensions) of the first contact between the two strands is assumed to be of the form K(n + m) = (n + m)−α−2L(n + m) with α ≥ 0 and L(⋅) slowly varying and corresponds to a loop with n bases in the first strand and m in the second. We study the localization-delocalization transition and we prove the existence of transitions inside the localized regime. We then present precise estimates on the path properties of the model. We then study the disordered version of the model by including a sequence of inde- pendent and identically distributed random variables with two indices. We focus on the influence of disorder on the denaturation transition: we want to determine whether the presence of randomness modifies the critical properties of the system with respect to the homogeneous case. We prove that the disorder is irrelevant if α < 1. We show also that for α > 1, the quenched and annealed critical points differ (basing on coarse graining techniques and fractional moment method), proving the presence of a relevant disorder regime.

Globally Asynchronous Locally Synchronous (GALS) Field-Programmable Gate Array (FPGA) are composed of standard synchronous reconfigurable logic islands that communicate with each other via an asynchronous means. Past research into fully asynchronous FPGA has demonstrated high throughput and reliability adopting dual-rail encoding. GALS FPGAs have been proposed, relying on bundled-data encoding and fixed asynchronous communication between synchronous islands. This thesis proposes a new GALS FPGA architecture with fully reconfigurable asynchronous fabric, that relies on coarse-grained Configurable Logic Blocks (CLBs) to improve the communication capability of the device. Through datapath dedicated elements, asynchronous pipelines are efficiently mapped onto the device. The architecture is presented as well as the customized tool flow needed to compile Verilog for this new coarse-grained reconfigurable circuit.The main purpose of this thesis is to map communication-purpose user-circuits on the proposed asynchronous fabric and evaluate their performance. The benchmark circuits target the design of a Networkon-Chip (NoC) router and employ two-phase bundled-data protocol. The results are obtained through simulation and compared with the performances of the same circuits on a fine-grained classical FPGA style. The proposed architecture achieves up to 3.2x higher throughput and 2.9x lower latency than the classical one. The results show that the coarse-grained style efficiently maps asynchronous communication circuits, and it may be the starting point for future reconfigurable GALS systems. Future work should focus on improving the back-end synthesis and evaluating the FPGA GALS system as a whole. / Globala Asynkrona Lokalt Synkrona (GALS) FPGAer består av standardiserade synkrona rekonfigurerbara logiska öar som kommunicerar med varandra på ett asynkront sätt. Tidigare forskning om helt asynkrona FPGAer har demonstrerat att hög genomströmning och tillförlitlighet kan erhållas mha sk dual-rail kodning. GALS FPGA har också föreslagits, där man istället förlitar sig på kodad data och fast asynkron kommunikation mellan synkrona öar. Denna avhandling föreslår en ny GALS FPGA-arkitektur med en omkonfigurerbar asynkron struktur, bestående av sk Coarse-grained CLBs för att förbättra kommunikationsförmågan på enheten. Genom att datavägarna använder sig av dedikerade element, kan asynkrona pipelines mappas effektivt på enheten. Arkitekturen presenteras liksom det verktygsflöde som behövs för att kompilera Verilog för denna nya grovkornigt omkonfigurerbara krets.Huvudsyftet med denna avhandling är att mappa kommunikationskretsar på den föreslagna asynkrona strukturen och utvärdera dess prestanda. Referenskretsarna som används för utvärdering är en NoC router som använder sig av ett tvåfas kommunikationsprotokoll. Resultaten erhålls genom simulering och jämförs med prestanda av samma krets implementerad i en finkornig klassisk FPGA-stil. Den föreslagna arkitekturen uppnår ca 3.2x högre genomströmning och 2.9x lägre latens än den klassiska. Resultaten visar att en grovkornig stil kan mappa asynkrona kommunikationskretsar på ett effektivt sätt, och att det kan vara en bra utgångspunkt för framtida omkonfigurerbara GALS-system.Framtida arbete bör fokusera på att förbättra back-end-syntesen och att utvärdera FPGA GALS-systemet i sin helhet.

Erosion of a river bed has important implications with respect to scour around river structures such as bridges, transport of contaminants attached to the sediment, and disruption or destruction of aquatic habitats. Erosion occurs when the resistive strength of the sediment is overcome by the hydrodynamic forces produced by the flow of water. This resistance to erosion in a sediment originates from gravity or interparticle forces for coarse sediment (sand and gravel) and fine sediment (silt and clay), respectively. Since the erosion of fine sediment depends on the combination of many interparticle forces, and this combination fluctuates widely amongst different fine sediments, past studies have had difficulty finding a consistent method to estimate fine sediment erosion. This study analyzes sediments that fall in the transition size range between fine and coarse sediments and compares the findings with those from fine sediments (Wang 2013) and sandy coarse sediments (Navarro 2004, Hobson 2008), in order to correlate the erosion rates of both sediment types to their physical characteristics. In this study, kaolin-sand mixtures were prepared by mixing various percentages of Georgia kaolin by weight ranging from 30% to 100% with industrial fine sand and tap water. Geotechnical and other tests of sediment properties were performed to measure water content, bulk density, grain size distribution, temperature, pH, and conductivity of these mixtures. Hydraulic flume experiments measured the erosion rates of each sediment and these rates were used to estimate the critical shear stress correlating to that mixture. Relationships between the physical properties of the sediment and critical shear stress were developed by multiple regression analysis. An alternative option of estimating the critical shear stress by a weighted equation, which uses the combination of fine sediment erosion and coarse sediment erosion equations separately, was explored and found to be a viable and accurate option to estimating both coarse and fine sediment erosion from the same parameters and equation. The results from this study can be used to estimate sediment erodibility and thus river bed stability based on simple tests of physical properties of the river bed sediment and will help predict scour around bridges and other flow obstructions.

This thesis considers coarse-grained models of DNA and RNA, developed in particular to study nanotechnological applications as well as some important biophysical processes. We first introduce sequence-dependent thermodynamics into a previously developed coarse-grained rigid base-pair model of DNA. This model is then used to study sequence-dependent effects in multiple DNA systems including: the heterogeneous stacking transition of single strands, the fraying of a duplex, the effects of stacking strength in the loop on the melting temperature of hairpins, the force-extension curve of single strands, and the structure of a kissing-loop complex. We further apply the DNA model to study in detail the properties of an autonomous unidirectionally propagating DNA nanotechnological device, called the ``burnt bridges motor''. We then apply the coarse-graining methods developed for the DNA model to construct a new sequence-dependent coarse-grained model of RNA, which aims to capture basic thermodynamic, structural and mechanical properties of RNA molecules. We test the model by studying its thermodynamics for a variety of secondary structure motifs and also consider the force-extension properties of an RNA duplex. This RNA model allows for efficient simulations of a variety of RNA systems up to hundreds or even thousands of base-pairs. Its versatility is further demonstrated by studying the thermodynamics of a pseudoknot folding, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin.

In Statistical Machine Translation (SMT), inference needs to be performed over a high-complexity discrete distribution de ned by the intersection between a translation hypergraph and a target language model. This distribution is too complex to be represented exactly and one typically resorts to approximation techniques either to perform optimisation { the task of searching for the optimum translation { or sampling { the task of nding a subset of translations that is statistically representative of the goal distribution. Beam-search is an example of an approximate optimisation technique, where maximisation is performed over a heuristically pruned representation of the goal distribution. For inference tasks other than optimisation, rather than nding a single optimum, one is really interested in obtaining a set of probabilistic samples from the distribution. This is the case in training where one wishes to obtain unbiased estimates of expectations in order to t the parameters of a model. Samples are also necessary in consensus decoding where one chooses from a sample of likely translations the one that minimises a loss function. Due to the additional computational challenges posed by sampling, n-best lists, a by-product of optimisation, are typically used as a biased approximation to true probabilistic samples. A more direct procedure is to attempt to directly draw samples from the underlying distribution rather than rely on n-best list approximations. Markov Chain Monte Carlo (MCMC) methods, such as Gibbs sampling, o er a way to overcome the tractability issues in sampling, however their convergence properties are hard to assess. That is, it is di cult to know when, if ever, an MCMC sampler is producing samples that are compatible iii with the goal distribution. Rejection sampling, a Monte Carlo (MC) method, is more fundamental and natural, it o ers strong guarantees, such as unbiased samples, but is typically hard to design for distributions of the kind addressed in SMT, rendering an intractable method. A recent technique that stresses a uni ed view between the two types of inference tasks discussed here | optimisation and sampling | is the OS approach. OS can be seen as a cross between Adaptive Rejection Sampling (an MC method) and A optimisation. In this view the intractable goal distribution is upperbounded by a simpler (thus tractable) proxy distribution, which is then incrementally re ned to be closer to the goal until the maximum is found, or until the sampling performance exceeds a certain level. This thesis introduces an approach to exact optimisation and exact sampling in SMT by addressing the tractability issues associated with the intersection between the translation hypergraph and the language model. The two forms of inference are handled in a uni ed framework based on the OS approach. In short, an intractable goal distribution, over which one wishes to perform inference, is upperbounded by tractable proposal distributions. A proposal represents a relaxed version of the complete space of weighted translation derivations, where relaxation happens with respect to the incorporation of the language model. These proposals give an optimistic view on the true model and allow for easier and faster search using standard dynamic programming techniques. In the OS approach, such proposals are used to perform a form of adaptive rejection sampling. In rejection sampling, samples are drawn from a proposal distribution and accepted or rejected as a function of the mismatch between the proposal and the goal. The technique is adaptive in that rejected samples are used to motivate a re nement of the upperbound proposal that brings it closer to the goal, improving the rate of acceptance. Optimisation can be connected to an extreme form of sampling, thus the framework introduced here suits both exact optimisation and exact iv sampling. Exact optimisation means that the global maximum is found with a certi cate of optimality. Exact sampling means that unbiased samples are independently drawn from the goal distribution. We show that by using this approach exact inference is feasible using only a fraction of the time and space that would be required by a full intersection, without recourse to pruning techniques that only provide approximate solutions. We also show that the vast majority of the entries (n-grams) in a language model can be summarised by shorter and optimistic entries. This means that the computational complexity of our approach is less sensitive to the order of the language model distribution than a full intersection would be. Particularly in the case of sampling, we show that it is possible to draw exact samples compatible with distributions which incorporate a high-order language model component from proxy distributions that are much simpler. In this thesis, exact inference is performed in the context of both hierarchical and phrase-based models of translation, the latter characterising a problem that is NP-complete in nature.

A molecular dynamics coarse-grained block copolymer (BCP) model was developed and used to studied directed self-assembly (DSA), especially in regards to applications for semiconductor manufacturing. Most of the thesis is spent investigating the effect that guiding layer properties and block copolymer properties have on line roughness and defect density in a BCP-DSA process. These two effects are perhaps the most critical in making BCP-DSA a cost efficient industrial process. It is found that guiding patterns have little effect on line roughness and in fact that the BCP heals the majority of roughness in the underlying pattern. BCP properties have a larger effect on line roughness. Segregation strength (as measured by χN, where χ is the Flory- Huggins interaction parameter and N is the degree of polymerization) resulted in a larger than expected increase in line roughness when χN was low. Polydispersity resulted in a moderate increase in line roughness. In regards to equilibrium defect density, free energy calculations showed that χ was the primary determining factor, not χN as many expected. Equilibrium defect density was found to decrease exponentially with increasing χ. Defect density is also found to scale exponentially with polydispersity. Concerning defect heal rate, which can increase the real defect rate of a process if said rate is too low, it is found that increasing χN linearly increased the barrier to defect healing, which means that the defect heal rate decreases exponentially. However, for thin films this is only true for χN > ~ 50. Below χN ~ 50, the barrier is approximately constant. These results give excellent guidance to the type of materials and processes necessary to optimize a BCP-DSA process. A simulation technique designed to more efficiently sample over energy barriers called protracted noise dynamics for polymer systems was developed and studied. It was found that a decrease in simulation time of up to 4 orders of magnitude was achieved. The effect of box size on allowable pitches for a lamellar forming BCP was derived and demonstrated. It was found that more elongated boxes yielded more possible pitches and more accurate results. A short study on the effect of multiblock copolymers on the location of the order-disorder transition was also carried out and it was found that multiblock copolymers had small effect on the ODT. The distribution of chain conformations was also calculated.