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1
Palau, Ortin David. "Dynamics of cellular decision making processes." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/396084.
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Cells, either as unicellular organisms or as part of a tissue of a multicellular organism, can acquire different functions thanks to their capability of changing their expression state. The enzyme synthesis, cell division or cell differentiation are some examples of these functions. The turning on and off of them lie in the mechanisms by which cells are able to integrate the information they perceive from the environment. Frequently, cells exhibit different responses under the same stimulus or environment. These probabilistic processes, whose behaviours are not univocal, are known as "cellular decision making". We can classify these processes according to the range at which the decision is made. We denominate cell-autonomous decision those in which of each cell chooses its response independently of the choice of the other cells of the population. By contrast, if the decision is made collectively by the whole population, it is classified as non autonomous. This second type of decisions involve mechanisms of cell-to-cell communication that mediate in the choices the cells and so, some spatial distributions of the different cell states can arise.
The capability of cellular decision making processes of performing a variety of responses under a same signal is given by the multistability and the stochasticity of their dynamics. While multistability is underlain by the nonlinear interactions of the elements involved in genetic regulation, stochasticity arises from the discrete nature of biochemical reactions and the thermal fluctuations of the cellular environment. These two characteristics motivate the study of these processes from Systems Dynamics the point of view, by identifying cell states with system attractors.
This Thesis focuses on the study of the general dynamical mechanisms that control cellular decision making processes. The main goal is to connect the properties of the decision with the relevant dynamical behaviour of the system while it is being made.
We have analysed the properties of cellular decisions in two systems: a system with cell-autonomous dynamics, where cells choose their state regardless the choice of the others; and a system where the decision is made jointly by all the tissue. In this second system, cells interact through a cell-to-cell communication that takes place at first neighbours. From these interactions, different pattern solutions arise, where different different cell types are spatially distributed along the tissue. Finally, it has been analysed the role that a specific choice, whose probability value is well known, plays in the functionality of an organism. The chosen system to study these consequences has been a process of differentiation that the parasite that causes malaria in humans performs.<br>Cada célula, ya se como organismo unicelular o formando parte de un organismo multicelular, tiene que desarrollar distintas funciones a lo largo de su vida. Algunos ejemplos de estas funciones son tales como la síntesis de encimas, dividirse o diferenciarse en otro tipo celular. La activación y desactivación de muchas de estas funciones está sujeta a la integración de la información que la célula percibe de su entorno. A menudo, las células exhiben respuestas distintas bajo un mismo estímulo o bajo unas mismas condiciones del entorno. Estos procesos probabilísticos son conocidos como "toma de decisiones celulares". Estos eventos celulares se puede desarrollar de forma autónoma por cada célula, o de forma colectiva por toda una población o tejido. En este segundo caso, se requiere de algún mecanismo que medie en la comunicación entre células.
Esta capacidad de estos sistemas de producir una variedad de respuestas es otorgada por la multiestabilidad y estocasticidad de sus dinámicas. Estas características motivan el estudio de estos procesos desde la perspectiva de la Dinámica de Sistemas, identificando los estados celulares a los atractores del sistema.
Esta Tesis se centra en el estudio de los mecanismos dinámicos genéricos que controlan la toma de decisiones celulares. Se ha caracterizado la conexión entre las propiedades de una decisión y el mecanismo subyacente que la genera. Dos tipos decisiones autónomas han sido analizadas de acuerdo a esta perspectiva. También se ha estudiado los mecanismos dinámicos que llevan a la selección de un patrón espacial concreto en un escenario de decisión no autónoma, en el que las células interactúan entre sí a primeros vecinos mediante una inhibición lateral. Estas decisiones han revelado como la simetría especial de la señal inductora de las mismas afecta a la solución final alcanzada por el tejido. Finalmente, se ha analizado el papel que la probabilidad de una decisión concreta y bien conocida puede desarrollar en la viabilidad del organismo implicado. El sistema de estudio escogido ha sido un proceso de diferenciación que lleva a cabo el parásito responsable de causar la malaria en humanos.
2
Herbert, Julian Richard. "Stochastic processes for parasite dynamics." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368164.
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Styles, M. J. "Predictive engineering processes for motorcycle dynamics." Thesis, Cranfield University, 2004. http://dspace.lib.cranfield.ac.uk/handle/1826/10715.
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This
study is an investigation into the use of computer aided handling and stability
analysis for motorcycles. In particular it considers Triumph Motorcycles Ltd., delving
into
Triumph's background, their strategy and the likelihood of them using virtual
techniques for stability and handling analysis.
Additionally, this work reviews current knowledge of motorcycle dynamics analysis
and builds on it.
A novel way of studying the steering feel has been developed by analysing the response
of the steer torque equation for the Sharp 1971 [1] and 1994 [2] models. The individual
contributors to this
equation are identified and the important ones are investigated
further. One conclusion of this study is that in reduced cornering and camber conditions
the steer
angle of the motorcycle, for a given steering input torque, increases when
compared to standard operating conditions. The steer angle also increases further as the
speed increases.
An update to a previous motorcycle model [3] has been made by revising the parameter
set, so that it is more applicable to a modem sports motorcycle. The rider model and
relaxation
length description have also been improved upon. The results show that the
new motorcycle has been made more manoeuvrable by the alterations to the parameters.
An optimal preview steering control system for cars [4] has been taken, improved upon
and used with the
newly developed motorcycle model discussed above. The results
from this novel work allow a designer to alter parameters and see how this affects the
motorcycles steering demands, path following, etc. It was shown that an increase in
the front wheel inertia makes the
motorcycle feel like the steering is heavier, and an
increase in the front wheel radius and wheelbase make the
steering feel lighter.
Future work into non-linear
analysis is recommended and improved rider and tyre
modelling is also desired.
4
Rué, Queralt Pau. "Transient and stochastic dynamics in cellular processes." Doctoral thesis, Universitat Politècnica de Catalunya, 2013. http://hdl.handle.net/10803/128333.
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This Thesis studies different cellular and cell population processes driven by non-linear and stochastic dynamics.
The problems addressed here gravitate around the concepts of transient dynamics and relaxation from a perturbed to a steady state. In this regard, in all processes studied, stochastic fluctuations, either intrinsically present in or externally applied to these systems play an important and constructive role, by either driving the systems out of equilibrium, interfering with the underlying deterministic laws, or establishing suitable levels of heterogeneity.
The first part of the Thesis is committed the analysis of genetically regulated transient cellular processes. Here, we analyse, from a theoretical standpoint, three genetic circuits with pulsed excitable dynamics. We show that all circuits can work in two different excitable regimes, in contrast to what was previously speculated.
We also study how, in the presence of molecular noise, these excitable circuits can generate periodic polymodal pulses due to the combination of two noise induced phenomena: stabilisation of an unstable spiral point and coherence resonance.
We also studied an excitable genetic mechanism for the regulation of the transcriptional fluctuations observed in some pluripotency factors in Embryonic Stem cells. In the embryo, pluripotency is a transient cellular state and the exit of cells from it seems to be associated with transcriptional fluctuations.
In regard to pluripotency control, we also propose a novel mechanism based on the post-translational regulation of a small set of four pluripotency factors. We have validated the theoretical model, based on the formation of binary complexes among these factors, with quantitative experimental data at the single-cell level. The model suggests that the pluripotency state does not depend on the cellular levels of a single factor, but rather on the equilibrium of correlations between the different proteins. In addition, the model is able to anticipate the phenotype of several mutant cell types and suggests that the regulatory function of the protein interactions is to buffer the transcriptional activity of Oc4, a key pluripotency factor.
In the second part of the Thesis we studied the behaviour of a computational cell signalling network of the human fibroblast in the presence of external fluctuations and signals. The results obtained here indicate that the network responds in a nontrivial manner to background chatter, both intrinsically and in the presence of external periodic signals. We show that these responses are consequence of the rerouting of the signal to different network information-transmission paths that emerge as noise is modulated.
Finally, we also study the cell population dynamics during the formation of microbial biofilms, wrinkled pellicles of bacteria glued by an extracellular matrix that are one of the simplest cases of self-organised multicellular structures. In this Thesis we develop a spatiotemporal model of cellular growth and death that accounts for the experimentally observed patterns of massive bacterial death that precede wrinkle formation in biofilms. These localised patterns focus mechanical forces during biofilm expansion and trigger the formation of the characteristic ridges. In this sense, the proposed model suggests that the death patterns emerge from the mobility changes in bacteria due to the production of extracellular matrix and the spatially inhomogeneous cellular growth. An important prediction of the model is that matrix productions is crucial for the appearance of the patterns and, therefore for winkle formation. We have also experimentally validated validated this prediction with matrix deficient bacterial strains, which show neither death patterns nor wrinkles.<br>En aquesta Tesi s’estudien diferents processos intracel·lulars i de poblacions cel·lulars regits per dinàmica estocàstica i no lineal. El problemes biològics tractats graviten al voltant el concepte de dinàmica transitòria i de relaxació d’un estat dinàmic pertorbat a l’estat estacionari. En aquest sentit, en tots els processos estudiats, les fluctuacions estocàstiques, presents intrínsecament o aplicades de forma externa, hi tenen un paper constructiu, ja sigui empenyent els sistemes fora de l’equilibri, interferint amb les lleis deterministes subjacents, o establint els nivells d’heterogeneïtat necessaris.
La primera part de la Tesi es dedica a l’estudi de processos cel·lulars transitoris regulats genèticament. En ella analitzem des d’un punt de vista teòric tres circuits genètics de control de polsos excitables i, contràriament al que s’havia especulat anteriorment, establim que tots ells poden treballar en dos tipus de règim excitable. Analitzem també com, en presència de soroll molecular, aquests circuits excitables poden generar polsos periòdics i multimodals degut a la combinació de dos fenòmens induïts per soroll: l’estabilització estocàstica d’estats inestables i la ressonància de coherència.
D’altra banda, estudiem com un mecanisme genètic excitable pot ser el responsable de regular a nivell transcripcional les fluctuacions que s’observen experimentalment en alguns factors de pluripotència en cèl·lules mare embrionàries. En l’embrió, la pluripotència és un estat cel·lular transitori i la sortida de les cèl·lules d’aquest sembla que està associada a fluctuacions transcripcionals. En relació al control de la pluripotència, presentem també un nou mecanisme basat en la regulació post-traduccional d’un petit conjunt de 4 factors de pluripotència. El model teòric proposat, basat en la formació de complexos entre els diferents factors de pluripotència, l’hem validat mitjançant experiments quantitatius en cèl·lules individuals. El model postula que l’estat de pluripotència no depèn dels nivells cel·lulars d’un únic factor, sinó d’un equilibri de correlacions entre diverses proteïnes. A més, prediu el fenotip de cèl·lules mutants i suggereix que la funció reguladora de les interaccions entre les quatre proteïnes és la d’esmorteir l’activitat transcripcional d’Oct4, un dels principals factors de pluripotència.
En el segon apartat de la Tesi estudiem el comportament d’una xarxa computacional de senyalització cel·lular de fibroblast humà en presència de senyals externs fluctuants i cíclics. Els resultats obtinguts mostren que la xarxa respon de forma no trivial a les fluctuacions ambientals, fins i tot en presència d’una senyal externa. Diferents nivells de soroll permeten modular la resposta de la xarxa, mitjançant la selecció de rutes alternatives de transmissió
de la informació.
Finalment, estudiem la dinàmica de poblacions cel·lulars durant la formació de biofilms, pel·lícules arrugades d’aglomerats de bacteris que conformen un dels exemples més simples d’estructures multicel·lulars autoorganitzades.
En aquesta Tesi presentem un model espai-temporal de creixement i mort cel·lular motivat per l’evidència experimental sobre l’aparició de patrons de mort massiva de bacteris previs a la formació de les arrugues dels biofilms. Aquests patrons localitzats concentren les forces mecàniques durant l’expansió del biofilm i inicien la formació de les arrugues característiques. En aquest sentit, el model proposat explica com es formen els patrons de mort a partir dels canvis de mobilitat dels bacteris deguts a la producció de matriu extracel·lular combinats amb un creixement espacialment heterogeni. Una important predicció del model és que la producció de matriu és un procés clau per a l’aparició dels patrons i, per tant de les arrugues. En aquest aspecte, els nostres resultats experimentals en bacteris mutants que no produeixen components essencials de la matriu, confirmen les prediccions.
5
Santos, Jaime Eduardo Moutinho. "Non-equilibrium dynamics of reaction-diffusion processes." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361994.
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Debacher, Nito Angelo. "Studies on the dynamics of wetting processes." Thesis, University of Bristol, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240354.
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7
Melander, Joshua. "On the dynamics of interacting spreading processes." Thesis, Kansas State University, 2016. http://hdl.handle.net/2097/34559.
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Master of Science<br>Department of Electrical and Computer Engineering<br>Faryad Darabi Sahneh<br>A significant number of processes we observe in nature can be described as a spreading process; any agent which is compelled to survive by replicating through a population, examples include viruses, opinions, and information. Accordingly, a significant amount of thought power has been spent creating tools to aid in understanding spreading processes: How do they evolve? When do they thrive? What can we do to control them? Often times these questions are asked with respect to processes in isolation, when agents are free to spread to the maximum extent possible given topological and characteristic constraints. Naturally, we may be interested in considering the dynamics of multiple processes spreading through the same population, examples of which there are no shortage; we frequently characterize nature itself by the interaction and competition present at all scales of life. Recently the number of investigations into interacting processes, particularly in the context of complex networks, has increased. The roles of interaction among processes are varied from mutually beneficial to hostel, but the goals of these investigations has been to understand the role of topology in the ability of multiple processes to co-survive. A consistent feature of all present works -- within the current authors knowledge -- is that conclusions of coexistence are based on marginal descriptions population dynamics.
It is the main contribution of this work to explore the hypothesis that purely marginal population descriptions are insufficient indicators of co-survival between interacting processes. Specifically, evaluating coexistence based on non-zero marginal populations is an over-simplistic definition. We randomly generate network topologies via a community based algorithm, the parameters of which allow for trivially controlling possibility of coexistence. Both marginal and conditional probabilities of each process surviving is measured by stochastic simulations. We find that positive marginal probabilities for both processes existing long term does not necessarily imply coexistence, and that marginal and conditional measurements only agree when layers are strongly anti-correlated (sufficiently distinct). In addition to the present thesis, this work is being prepared for a journal article publication.
The second portion of this thesis presents numerical simulations for the Adaptive Contact - Susceptible Alert Infected Susceptible model. The dynamics of interaction between an awareness process and an infectious process are computed over a multilayer network. The rate at which nodes "switch" their immediate neighbors (contacts) when exposed to the infection is varied and numerical solutions to the epidemic threshold are computed according to mean-field approximation. We find two unexpected cases where certain parameter configurations allow the epidemic threshold to either increase above or decrease below the theoretical limits of the layers when considered individually. These computations were performed as part of a separate journal article that has been accepted for publication.
8
Grasselli, Nora Ilona. "MBA learning group dynamics : Structures and processes." Jouy-en Josas, HEC, 2008. http://www.theses.fr/2008EHEC0010.
Full textAbstract:
Cette thèse vise à explorer la dynamique de petits groupes d’apprentissage autogérés et non-hiérarchiques au sein d’un programme MBA. A travers un processus inspiré de la recherche-action et de la psychosociologie, cette recherche se focalise d’abord sur deux hypothèses de travail : l’impact de la iversité et la fonction des espaces sociaux dans ces groupes. Cependant, cette recherche a permis de mettre en évidence que la question centrale dans ces groupes d’apprentissage serait leur design : la division du travail appropriée, la gestion du temps, et l’allocation des rôles. Les analyses complémentaires concernant la division du travail et la gestion du temps montrent que ces éléments du design peuvent aussi fonctionner comme stratégies protectrices contre les difficultés possibles que ces groupes d’apprentissage rencontrent pendant leur fonctionnement. Ainsi, cette recherche met en avant l’importance d’un design adaptatif et ses liens aves les processus internes dans les petits groupes. Cette thèse met aussi en évidence l’importance de la démarche de recherche-action, du moins de son esprit, qui permet de découvrir des phénomènes subtils et imprévus et de répondre aux critiques formulées à l’encontre des MBA, stigmatisant la normalisation des apprentissages et des comportements<br>This study explores the dynamics of small, non-hierarchical, self-managing learning groups in an MBA program. In the spirit of action research and psychosociology two initial working hypotheses, the impact of diversity on the groups and the use of social spaces, are examined. Nonetheless, it turns out that the central issue in the learning groups seems to be the groups’ design, e. G. The adequate division of labor, the management of time, and the allocation of roles. Further analyses on labor division and group time management show that these design features may also function as protective strategies against the possible difficulties the learning groups risk to encounter. Herewith this research puts forward the importance of adaptive group designs and their links with the internal processes in small groups. This study also emphasizes the value of action research for discovering subtle, unpredictable phenomena and for providing a possible response to the critiques addressed to the standardized learning and behaviors on MBA programs
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Redd, Preston T. "Market Dynamics with Non-Homogeneous Poisson Processes." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/3630.
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The Bertrand Duopoly model for demand in economics is a well-used model. Although this model has important insights towards pricing strategy, it does not accurately depict true market behaviors. In this paper, we will examine the advantages and disadvantages of the current model and its assumptions.We then take a whole new approach towards modeling this phenomena, using Poisson processes to model the demand of goods. We will discuss why this is a better approach and explain how we can extend this to better understand pricing strategies and market dynamics. We then apply our findings to the newsvendor problem, a commonly used problem in inventory management. Using non-homogeneous Poisson processes we explain how to find an optimal pricing strategy and an optimal inventory level for the newsvendor problem.In this paper we explain how to extend the newsvendor problem to a newsvendor duopoly problem. Again we show how to find the optimal pricing strategies and inventory levels for multiple goods in a market. Having found the optimal pricing strategy and inventory level, we then examine the market dynamics in more details. We explore monopolistic and duopolistic markets where the goods range from complements to substitutes and homogeneous to differentiated goods. We discuss how to model the progression of the inventory probabilities and then explain how to price inventory options.
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Eakin, H. J. W. "Ultrafast relaxation processes in semiconductors." Thesis, University of Oxford, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.382634.
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Evans, P. R. "Control techniques to improve rolling mill dynamics." Thesis, University of Bath, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285299.
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Lui, Ying Bik. "The fluid dynamics of pressure die casting processes." Thesis, Brunel University, 1997. http://bura.brunel.ac.uk/handle/2438/5224.
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The main text of the thesis consists of seven chapters. Following the literature survey, the work in Chapter 2 focuses on the study of the whole process of pressure die casting. The necessity of reclassification against the traditional 'three-stage' description is introduced in order to build a new basic tenet in constructing theoretical and practical investigations, which leads to the creation of fluid dynamic mathematical models of the process. On the basis of Chapter 2, Chapter 3 concentrates on dealing with the computer simulation of filling flow patterns occurring in the third stage that play the most important role in the process. The Simplified Marker And Cell (SMAC) method is used to obtain the computational results of the filling patterns of pressure die casting processes. On the basis of the computational analysis of typical examples, the viscosity, gravitational force and velocity effects on the overall filling pattern are examined, that lead to a validation of the important hypothesis that an ideal liquid can be used in numerical simulation of filling patterns and this enables one to achieve a more effective computer program for a complex cavity by quasi-3D or 3D models. Chapter 4 treats a specific problem of the residual flow that exists in the final (fifth) stage of the process. Mathematical models of residual flow are derived. Chapter 5 mainly consists of two parts. The first part deals with the application of similitude laws for simulating flows in pressure die casting processes. Detailed analyses and criteria on different relationships between model and prototype are given in order to correct previously offered formulae by Eckert (1989). The results of numerical simulation presented in Chapter 3 are also extended to validate the similitude criteria. The second part of Chapter 5 presents the use of a charge coupled device(CCD) for studying the diversity of fluid motion including the filling pattern, residual flow, thermals and air entrapment during cavity-fill and post cavity-fill within a one single shot cavity filling in water analogue experiments. A discussion, conclusions and suggestions for further study of the subject concerned are presented in Chapters 6 and Chapter 7.
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Privalov, Timofei. "Electronic and nuclear dynamics of X-ray processes." Doctoral thesis, Stockholm : Tekniska högsk, 2001. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3189.
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Schönborn, Jan Boyke [Verfasser]. "Dynamics of photoinduced switching processes / Jan Boyke Schönborn." Kiel : Universitätsbibliothek Kiel, 2013. http://d-nb.info/1031666966/34.
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Closkey, Cynthia. "Developing decision processes for managing supply chain dynamics." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/10478.
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Thesis (M.S.)--Massachusetts Institute of Technology, Sloan School of Management, 1997, and Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.<br>Includes bibliographical references (p. [57]).<br>by Cynthia Closkey.<br>M.S.
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Mendes, Renato Paulo dos Santos. "The Douro estuarine plume: detection, processes and dynamics." Doctoral thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/17073.
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Doutoramento em Física<br>O Douro é um dos maiores rios da Península Ibérica, constituindo a maior descarga de água
doce para o Oceano Atlântico na costa noroeste portuguesa. A sua pluma estuarina tem
particular relevância na dinâmica costeira e na modulação de fenómenos biogeoquímicos. São
objetivos desta dissertação contribuir para a compreensão dos processos físicos associados
à geração e propagação da pluma estuarina do Rio Douro no oceano, assim como para o
conhecimento dos seus padrões de dispersão e da forma como estes alteram a hidrologia
e a circulação costeira, considerando os agentes forçadores típicos deste fenómeno (caudal
fluvial, vento e maré) e índices climáticos relevantes. Para concretização destes objetivos
foram desenvolvidas e aplicadas metodologias inovadoras de processamento de dados de
deteção remota, assim como novas implementações estuarinas e costeiras de modelos
numéricos. Através de imagens MODIS, otimizadas para o estudo de fenómenos costeiros,
efetuou-se uma deteção rigorosa da pluma. Identificou-se uma relação entre o sinal túrbido
nLw555 e o caudal, demonstrando-se este produto como um bom proxy para a observação
da pluma no oceano. As escalas temporais e espaciais da pluma foram caraterizadas através
destas imagens, combinadas com dados de caudal fluvial, maré, vento e precipitação, e
também com índices climáticos relevantes. Para compreender a propagação da pluma e
caracterizar a sua dinâmica e impacto na circulação costeira, foi desenvolvida uma aplicação
3D de modelos estuarinos e costeiros com malhas aninhadas de resolução variável. Definiramse
e analisaram-se diferentes cenários de vento e descarga fluvial. A interação da pluma do
Rio Douro e do Minho foi ainda analisada através dos resultados de simulações baseadas num
evento de inverno. Os compósitos túrbidos mostraram que a pluma é facilmente detetada
quando o caudal é maior que 500 m3 s1. A descarga fluvial e o vento são os principais
forçadores da sua propagação, enquanto a maré é apenas importante na região próxima à
embocadura do estuário. Observaram-se relações a uma escala interanual entre a turbidez da
pluma e os índices climáticos East Atlantic e NAO, com uma correlação máxima identificada
com 1 e 3 meses de desfasamento, respetivamente. Com base nos resultados das simulações
efetuadas, a pluma é classificada como de larga escala e de adveção superficial, apresentando
características de uma pluma prototípica. Em condições de caudal moderado a elevado, a
descarga estuarina é suficiente para gerar uma corrente costeira para norte sem ação do
vento. Em eventos de ventos leste, a propagação da pluma é similar ao caso sem vento,
com um aumento da velocidade da corrente. Uma corrente costeira para sul é unicamente
identificada sob condições de forte vento de oeste. Ventos de norte tendem a estender
a pluma para o largo, com uma inclinação na direção sudoeste, enquanto ventos de sul
intensificam a corrente para norte, sendo a mistura das plumas do Douro e do Minho uma
consequência possível. A análise desta interação apontou a contribuição do Douro como
importante na estabilização da WIBP e nas trocas de água entre o oceano e as Rias Baixas.
A interação da pluma do Douro com estuários localizados a sul da sua foz e a confirmação in
situ da recirculação observada nos resultados numéricos afiguram-se como temas relevantes
para investigações futuras.<br>The Douro is one of the largest rivers of the Iberian Peninsula, representing the most
important freshwater input into the Atlantic Ocean (on the northwestern Portuguese coast).
Its estuarine plume has particular relevance on coastal dynamics and biogeochemistry. The
main goal of this dissertation is to contribute to increase knowledge on physical processes
associated with the generation and propagation of the Douro estuarine plume. The general
patterns of dispersion in the ocean and how the plume change hydrography and coastal
circulation were also evaluated, considering the typical drivers involved (river discharge, wind
and tide) and relevant climate indices. Innovative methodologies to process remote sensing
data, as well as new implementations of high-resolution estuarine and coastal numerical
models have been developed and applied. The plume was detected through MODIS images,
optimized for coastal studies. The relation between the turbid nLw555 signal and river
discharge was identified, demonstrating that this product is a good proxy for the observation
of the Douro estuarine plume in the coastal ocean. An interconnected approach, combining
these images, river discharge, tide, wind and precipitation data, as well as relevant climate
indices, was used to study the temporal and spatial scales of the plume. The implementation
of estuarine and coastal models with nested domains of variable resolution was developed
to understand the plume propagation and characterize its dynamics and impact on coastal
circulation. Using these applications, different scenarios of wind and river discharge were
defined and analysed. The interaction of the Douro and the Minho estuarine plumes was
further evaluated through simulations based on a winter event. Turbid composites showed
that the plume is easily detected when river discharge is greater than 500 m3 s1. River
discharge and wind are the main driver acting on the plume propagation, whilst tidal effect is
only important near the estuary mouth. A relation between turbid plume and climate indices
East Atlantic (EA) and North Atlantic Oscillation (NAO) was observed at inter-annual scale,
with a maximum correlation identified at 1 and 3-month lags, respectively. The Douro
estuarine plume is classified as large-scale and surface-advected, presenting characteristics
of a prototypical plume, based on the results of the numerical simulations. The estuarine
outflow is sufficient to generate a northward coastal current without wind action under
moderate-to-high river discharge conditions. Under easterly winds, the propagation pattern
is similar to the case without wind forcing, with a slight increase in the northward current.
A southward coastal current is only generated by strong westerly winds. Under upwellingfavourable
winds, the plume extends offshore with tilting towards southwest. Southerly
winds increase the velocity of the northward current, being the merging of the Douro and
Minho estuarine plumes a likely consequence. The analysis of this interaction pointed out
the Douro as an important contributor to the WIBP stabilization and in the water exchange
between ocean and Rias Baixas. The interaction of the Douro estuarine plume with estuaries
located south of its inlet and the in situ confirmation of the re-circulation bulge observed in
numerical results seem as relevant for future research topics.
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Crocker, Gregory Bruce. "Physical processes in Antarctic landfast sea ice." Thesis, University of Cambridge, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.278282.
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Schaub, Michael Thomas. "Unraveling complex networks under the prism of dynamical processes : relations between structure and dynamics." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/38446.
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We consider relations of structure and dynamics in complex networks. Firstly, a dynamical perspective on the problem of community detection is developed: how to partition a graph into sets of nodes which have stronger relations to each other than to other nodes in the network. We show how several approaches to this problem can be re-interpreted from a dynamical perspective. It is demonstrated how this perspective can circumvent limitations of commonly used, structure based community detection methods such as Modularity or the map-equation, which are prone to over-partition communities of large effective diameter. Secondly, we present graph-theoretical measures to quantify edge-to-edge relations, inspired by the notion of flow redistribution induced by edge failures. We demonstrate how our measures can reveal the dynamical interplay between the edges in a network, including potentially non-local interactions. We showcase the general applicability of our edge-centric measures through analyses of several example systems from different areas. Finally, relations between structure and dynamics are discussed in the context of neural networks. We show how the topology of networks of leaky-integrate-and-fire neurons can be changed such that a 'slow-dynamics' arises, in which groups of neurons vary their firing rates coherently, and discuss how this is reflected in spectrum of the network's coupling matrix. We further consider the problem of detecting cell assemblies, groups of neurons which share a more similar temporal activity pattern when compared to members of other groups, in time series of neural firing events. Using a biophysically inspired pairwise coupling measure we can infer a functional network from the data, and map the task of finding cell assemblies onto a community detection problem, which can be solved within our dynamical framework.
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Nystedt, Björn. "Evolutionary Processes and Genome Dynamics in Host-Adapted Bacteria." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-107720.
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Many bacteria live in close association with other organisms such as plants and animals, with important implications for both health and disease. This thesis investigates bacteria that are well adapted to live inside an animal host, and describes the molecular evolutionary processes underlying host-adaptation, based on bacterial genome comparisons. Insect-transmitted bacteria of the genus Bartonella infect the red blood cells of mammals, and we investigate host adaptation and genome evolution in this genus. In Bartonella, many host-interaction systems are encoded in a highly variable chromosomal segment previously shown to be amplified and packaged into bacteriophage particles. Among all genes imported into the Bartonella ancestor, we identify the short gene cluster encoding these phage particles as the most evolutionary conserved, indicating a strong selective advantage and a role in niche adaptation. We also provide an overview of the remarkable evolutionary dynamics of type IV and type V secretion systems, including a detailed analysis of the type IV secretion system trw. Our results highlight the importance of recombination and gene conversion in the evolution of host-adaptation systems, and reveal how these mutational mechanisms result in strikingly different outcomes depending on the selective constraints. In the insect endosymbionts Buchnera and Blochmannia, we show that genes frameshifted at poly(A) tracts can remain functional due to transcriptional slippage. Selection against poly(A) tracts is very inefficient in these genomes compared to other bacteria, and we discuss why this can lead to increased rates of gene loss. Using the human pathogen Helicobacter pylori as a model, we provide a deeper understanding of why highly expressed genes evolve slowly. This thesis emphasizes the power of using complete genome sequences to study evolutionary processes. In particular, we argue that knowledge about the complex evolution of duplicated gene segments is crucial to understand host adaptation in bacteria.
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Hoffecker, Ian Torao. "Decoupling Interdependent Cytoskeletal Processes to Control Cell Adhesion Dynamics." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/193582.
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Palaniswaamy, Geethpriya. "DSMC multicomponent aerosol dynamics sampling algorithms and aerosol processes /." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4737.
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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.<br>The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed Dec. 12, 2007). Vita. Includes bibliographical references.
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Shepherd, Tricia D. "Models for chemical processes : activated dynamics across stochastic potentials." Diss., Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/27062.
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King, Simon. "Ultrafast processes and excited state dynamics in conjugated polymers." Thesis, Durham University, 2008. http://etheses.dur.ac.uk/2192/.
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The photophysics of a number of conjugated polymers used in organic display applications has been studied using ultrafast techniques. An updated method for measuring the intersystem crossing rate was developed. This has been used to measure the intersystem crossing in a number of conjugated polymers and oligomers. It was found that as expected the intersystem crossing in conjugated polymers is generally very low. The intersystem crossing in a molecule that exhibits dual fluorescence depending on the polarity of the environment was investigated. In polar solvents when the molecule forms a twisted interconnected charge transfer state the intersystem crossing rate was found to be ten times that of the planer locally excited state found in non-polar media. The nature of charge generation in conjugated polymers has also been investigated, it was found that in the prototypical conjugated polymer, polyfluorene, there is no intrinsic charge photogeneration. However, charges can be formed by singlet-singlet annihilation reactions. This is made very efficient in the solid state by the rapid diffusion and migration of excitons. The photophysics of a novel polyfluorene, polyspirobifluorene, was investigated thoroughly; it has been found that the addition of the spiro side group containing electron-donating groups causes a charge transfer state to form between the backbone and the side group. This can act as a reservoir for the emissive singlets, thus giving the polymer a long tail in the fluorescence decay. Finally, ultrafast pump probe spectroscopy was used to investigate on chain migration of excitons in dilute solutions of a ladder type polymer. The migration to the lowest energy segment of the chain shows up as a shift to the red of the photobleaching signal in the pump probe spectrum. This shows that the low energy states become occupied after the initial excitation, as the high energy states become depopulated by the migration, this process taking about 6.2ps.
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Fahrenkopf, Max A. "Optimization, Dynamics and Stability of Non-Linear Separation Processes." Research Showcase @ CMU, 2014. http://repository.cmu.edu/dissertations/390.
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In this thesis we develop a non convex non-linear programming problem that determines the minimum run time of a rapid, gel-free DNA separation technique called micelle end-labeled free solution electrophoresis (ELFSE). Micelle ELFSE is typically performed in capillary electrophoresis where the capillary length, electric field strength, and micelle drag tag size are the primary tuning variables. Using optimization, we demonstrate that capillary electrophoresis can be used to separate up to 600 bases in under 50 minutes. A significant improvement in performance is then shown to be achievable by using parallel capillaries which can separate up to 600 bases in under 5 minutes. Even more improvement is shown to be possible by using alternative separation modes, such as using an EOF counter- ow which enables 600 bases to be separated in under 4.5 minutes using a single capillary, and microfluidics utilizing snapshot detection to yield 600 bases in under 3.5 minutes. Long DNA, above 5000 bases, is particularly challenging to separate quickly. Using Brownian dynamics simulations we show the viability of integrating two DNA separation techniques: end-labeled DNA electrophoresis and entropic trapping. We present simulation results that demonstrate improved performance of the integrated device over entropic trapping alone. Brownian dynamics simulations are very computationally expensive, often taking over 24 hours per data point. We present an acceleration technique called projective integration which may be useful for simulations with a large amount of integration steps. We show that, using a model built from linear regression, periodic extrapolations can be used to decrease computational time. Finally we present the stability of the multi-component distillation column. We demonstrate, through the use of thermodynamics, that the distillation column is asymptotically stable when using pressure, temperature, and level control on the reboiler and condenser.
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Collins, Charine. "The dynamics and physical processes of the Comoros Basin." Doctoral thesis, University of Cape Town, 2013. http://hdl.handle.net/11427/6467.
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Includes abstract.<br>Includes bibliographical references.<br>The main objective of this thesis was to investigate the circulation in the ComorosBasin using observed and model datasets. These data were used to establish whether or not a Comoros Gyre exists and to investigate the nature of the eddy variability in the basin.The water masses in the Comoros Basin emulate those found further south in the Mozambique Channel. The presence of AAIW north of Madagascar confirmed that this water mass enters the Comoros Basin from the east while the presence of North Atlantic Deep Water showed that this water mass is capable of spreading northward over the Davie Ridge. The main currents in the Comoros Basin, the westward flowing NEMC and a poleward current along the western boundary, are under the influence of the monsoon winds. The NEMC intensifies during the Southwest monsoon in response to a strong wind jet which develops off the northern tip of Madagascar, whereas the poleward current weakens due to the opposing force imposed by the southwesterlies. Additionally, the circulation in the basin consist of meso-scale eddies of both polarities. Anti-cyclonic eddies, with lifespans of
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Karrasch, Daniel. "Hyperbolicity & Invariant Manifolds for Finite-Time Processes." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-97207.
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The aim of this thesis is to introduce a general framework for what is informally referred to as finite-time dynamics. Within this framework, we study hyperbolicity of reference trajectories, existence of invariant manifolds as well as normal hyperbolicity of invariant manifolds called Lagrangian Coherent Structures. We focus on a simple derivation of analytical results. At the same time, our approach together with the analytical results has strong impact on the numerical implementation by providing calculable expressions for known functions and continuity results that ensure robust computation. The main results of the thesis are robustness of finite-time hyperbolicity in a very general setting, finite-time analogues to classical linearization theorems, an approach to the computation of so-called growth rates and the generalization of the variational approach to Lagrangian Coherent Structures.
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Linkmann, Moritz Frederik Leon. "Self-organisation processes in (magneto)hydrodynamic turbulence." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/19572.
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Self-organising processes occurring in isotropic turbulence and homogeneous magnetohydrodynamic (MHD) turbulence are investigated in relation to the stability of helical flow structures. A stability analysis of helical triad interactions shows that compared to hydrodynamics, equilibria of the triadic evolution equations have more instabilities with respect to perturbations on scales larger than the characteristic scale of the system. Some of these instabilities can be mapped to Stretch-Twist-Fold dynamo action and others to the inverse cascade of magnetic helicity. High levels of cross-helicity are found to constrain small-scale instabilities more than large scale instabilities and are thus expected to have an asymmetric damping effect on forward and inverse energy transfer. Results from a numerical investigation into the influence of helicity on energy transfer and dissipation are consistent with this observation. The numerical work also confirms the predictions of an approximate method describing the Reynolds number dependence of the dimensionless dissipation coefficient for MHD turbulence. These predictions are complemented by the derivation of mathematically rigorous upper bounds on the dissipation rates of total energy and cross-helicity in terms of applied external forces. Large-scale helical flows are also found to emerge in relaminarisation events in direct numerical simulations of isotropic hydrodynamic turbulence at low Reynolds number, where the turbulent fluctuations suddenly collapse in favour of a large-scale helical flow, which was identified as a phase-shifted ABC-flow. A statistical investigation shows similarities to relaminarisation of localised turbulence in wall-bounded parallel shear flows. The turbulent states have an exponential survival probability indicating a memoryless process with a characteristic lifetime, which is found to depend super-exponentially on Reynolds number akin to well-established results for pipe and plane Couette flow. These and further similarites suggest that the phase space dynamics of isotropic turbulence and wall-bounded shear flows are qualitatively similar and that the relaminarisation of isotropic turbulence can also be explained by the escape from a chaotic saddle.
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Luse, Christopher. "Dynamics of epitaxial growth and recovery." Diss., Georgia Institute of Technology, 1994. http://hdl.handle.net/1853/27651.
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Xu, Danya. "Lagrangian Study of Particle Transport Processes in the Coastal Gulf of Maine." Fogler Library, University of Maine, 2008. http://www.library.umaine.edu/theses/pdf/XuD2008.pdf.
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Ferri, Silvia. "Stochastic processes for natural evolutionary dynamics of T-cell repertoires." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019.
Find full textAbstract:
Il sistema immunitario è un esempio di un sistema biologico caratterizzato da varie scale di complessità che può essere modellizzato con un approccio fisico ricorrendo agli strumenti dei sistemi complessi, e in particolare ai processi stocastici.
Si tratta di un argomento indubbiamente affascinante, dal momento che il sistema immunitario gioca un ruolo fondamentale nel proteggere l’organismo dalle minacce esterne. In particolare la parte del sistema immunitario cosiddetta adattiva, di cui fanno parte le T-cells, è in grado di produrre una risposta specifica modulando costantemente il numero di cellule che esprimono ciascun recettore, in base al variare della composizione del pool di patogeni con cui l’organismo interagisce. Dunque le T-cells formano un insieme, detto repertorio, in continua evoluzione, che contiene informazioni sulle sfide affrontate dal sistema immunitario di un individuo.
Oltre a poter modellizzare la risposta a uno stimolo specifico, come può essere un’infezione o un vaccino, altrettanto importante come punto di partenza è investigare il funzionamento di base del sistema immunitario in individui sani. Il presente lavoro si propone dunque di studiare la dinamica naturale del repertorio delle T-cells, intesa come l’evoluzione dinamica quando l’interazione con l’ambiente non è dominata da uno stimolo forte e preciso. Inserendosi nel solco tracciato dai modelli stocastici per il sistema immunitario, lo scopo è quello di analizzare dati di individui sani e identificare una dinamica stocastica di base, con un approccio data-driven.
A questo scopo vengono considerati diversi modelli che tengono conto della stocasticità intrinseca nel sistema o dell’interazione con l’ambiente, e viene costruita un’analisi che permette di discriminare quale sia il meccanismo dominante. Viene inoltre tracciato un quadro di inferenza statistica per determinare i parametri di tali modelli.
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Vilà, Casanovas Arnau. "Quantum dynamics of physicochemical processes in superfluid (4)He nanodroplets." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/313040.
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The present thesis presents several theoretical studies on the dynamical processes of physicochemical interest involving superfluid helium (4He) nanodroplets. It has been developed a theoretical approach and computationally implemented. This consists in the first stage on the theoretical study of chemical reaction dynamics in superfluid helium nanodroplets.
The description of the system is fully quantum and consists in a hybrid method in which different theoretical approaches are combined to describe the different components of the system. The liquid helium (superfluid) has been described through the Density Functional Theory (DFT), using a phenomenological energy functional. Atomic and molecular impurities have been described by means of standard quantum dynamics.
The methodology developed in the present thesis has been applied to the study of various physicochemical processes of interest. These studies con be grouped as:
- Study of the structure, energy and electronic spectroscopy of helium nanodroplets doped with atomic oxygen in different electronic states. In this work, the influence of the electronic state of oxygen and energy structure of the drop has been determined to be the induction of anisotropy on the helium density (for the open-shell cases), as well as the high quality of helium nanodroplets acting as a matrix for high-resolution spectroscopy confirmed.
- Investigation on the dynamics of the photodissociation of homonuclear diatomic molecules in superfluid helium nanodroplets. In this context, the method developed has been initially applied to the case of molecular chlorine. Some interesting results related with the energy exchange phenomenon and generation of quantum (confined) resonances due tot the interaction of the molecules with the helium nanodroplet have been reported. Moreover, the relaxation process of the nanodroplet after the photodissociation has been also studied. This methodology developed has been also applied to the case of two halogen homonuclear diatomic molecules more, Br2 and I2. Different phenomenology and mechanism have been found for these cases, even producing full recombination for the biggest droplet considered. Furthermore, in order to determine the role played by the mass of the atoms of the diatomic homonuclear molecule on this process, we have studied the photodissociation dynamics of prototypic “isomers” of Cl2.
- We have modeled the process of the capture of a neon atom by superfluid helium nanodroplets. We have restricted to the case of zero angular momentum as a first approach to the problem at the quantum level. We obtained the time scale of this process. Also, it was found that the energy exchange does not take place at any time, but until the velocity is low enough (Landau’s critical velocity) there is no mechanism for the exchange energy. This leads to a constant (mean) velocity of the quantum particle (Ne atom), since the friction force is zero. The resulting wave packet in momentum representation has a Gaussian type profile.
- The synthesis reaction of a dimer of van der Waals (Ne2) in helium nanodroplets has been investigated. This process starts with a drop initially doped with Ne atom. Then, a second Ne atom is captured, which initiates the process of the synthesis. We have restricted to the zero angular momentum case for computational reasons. A great variety of phenomenology (reaction mechanisms) depending on the collision velocity and the droplet size has been found.<br>La present Tesi doctoral comprèn diferents estudis teòrics sobre processos fisicoquímics relacionats amb nanogotes d'heli (4He) superfluid. Per a la seva realització s'ha desenvolupat la metodologia teòrica i implementat a nivell computacional. Es tracta d'un primer estudi teòric en qual s'estudia la dinàmica de reaccions químiques en nanogotes d'heli superfluid.
La descripció del sistema és completament quàntica, combinant diferents aproximacions teòriques per descriure els components del sistema. L'heli líquid s'ha descrit a través de la teoria del funcional de la densitat (DFT), utilitzant un funcional fenomenològic. Les impureses atòmiques i moleculars s'han descrit mitjançant dinàmica quàntica.
La metodologia desenvolupada ha estat aplicada a l'estudi de diversos processos d'interès quimicofísic. Aquests són:
- Estudi de l'estructura, energètica i espectroscòpia electrònica de nanogotes d'heli dopades amb oxigen atòmic en diferents estats electrònics.
- Estudi de la dinàmica de la fotodissociació de molècules diatòmiques homonuclears en nanogotes d'heli superfluid. El mètode desenvolupat s'ha aplicat inicialment al cas del clor molecular. Posteriorment s'ha realitzat els casos del brom i el iode, així com d'"isòtops" artificials del clor amb l'objecte de determinar la influència de la massa sobre aquest tipus de processos. S’ha pogut determinar la formació de ressonàncies quàntiques, les qual s’han estudiat amb detall posteriorment.
- Modelització del procés de captura d'un àtom de neó per part de nanogotes d'heli superfluid. S'ha estudiat el cas de moment angular nul com una primera aproximació a la problemàtica a nivell quàntic.
- Reacció de síntesi d'un dímer de van der Waals (Ne2) en nanogotes d'heli. Partint d'una gota inicialment dopada amb un àtom de Ne, la captura d'un segon àtom de Ne inicia el procés de la síntesi. S'ha determinat una gran varietat de fenomenologia (mecanismes de reacció) segons la velocitat de col·lisió i la mida de la gota.
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Pesce, Lorenzo. "Dissipative quantum dynamics of elementary chemical processes at metal surfaces." [S.l. : s.n.], 1998. http://darwin.inf.fu-berlin.de/1998/4/index.html.
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Long, Xinhua. "Loss of contact and time delay dynamics of milling processes." College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/3421.
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Thesis (Ph.D.) -- University of Maryland, College Park, 2006.<br>Thesis research directed by: Mechanical Engineering. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Pischke, Philipp [Verfasser]. "Modeling of collisional transport processes in spray dynamics / Philipp Pischke." Aachen : Hochschulbibliothek der Rheinisch-Westfälischen Technischen Hochschule Aachen, 2014. http://d-nb.info/1058348051/34.
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Gutsell, S. L. "Understanding forest dynamics incorporating both local and regional ecological processes." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq64863.pdf.
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Gaige, Elizabeth. "Throughfall Dynamics and Canopy Processes in a Nitrogen Fertilized Forest." Fogler Library, University of Maine, 2005. http://www.library.umaine.edu/theses/pdf/GaigeES2005.pdf.
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Miao, Quan. "Nuclear Dynamics in Linear and Non-linear X-ray Processes." Doctoral thesis, KTH, Teoretisk kemi och biologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-133432.
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New generations of brilliant synchrotron radiation sources and intense X-ray and optical lasers have opened unprecedent opportunities in linear and non-linear spectroscopies of molecules. This together with new instrumentation calls for further development of theory to explain observations and suggest new experiments. These two goals are the main objectives of the present thesis. In the first part of the thesis we study resonant inelastic X-ray scattering of the oxygen molecule. Recent experimental data of O2 show the dependence of the vibrational profile on the polarization of the X-rays. This vibrational scattering anisotropy is explained by the interference of the resonant and nonresonant inelastic scattering channels in O2. The second part of the thesis explores X-ray lasing caused by ultrafast dissociation of the HCl molecule in a repulsive core-excited state pumped by an X-ray free-electron laser. We show that the lasing efficiency is drastically enhanced due to the self-trapping of the amplified pulse into the ridge of the gain. The third part of the thesis is devoted to another non-linear phenomenon - optical limiting. Our time-dependent simulations are in agreement with the experimental data and show that phthalocyanines with heavy central metals exhibit good optical limiting properties for nanosecond pulses. Symmetry and the symmetry breaking are important fundamental concepts in physics, chemistry and biology. In the next part of the thesis we study theoretically the novel symmetry breaking mechanism in resonant Auger scattering. Both theory and electron-ion coincidence measurements for the oxygen molecule evidence the symmetry breaking of the oxygen cation caused by momentum exchange between the fast Auger electron and counter propagating dissociating oxygen atoms. The last part of the thesis is devoted to the role of the rotational degrees of freedom in X- ray ionization of molecules. We present here new results related to the rotational Doppler and angular recoil effects in X-ray ionization using the N2 and HCl molecules as illustrating examples. The dependence of the ionization cross section on the direction of ejection of fast electrons explains the sensitivity of the rotational broadening to the final state and to the polarization of X-rays observed recently for the N2 molecule. The theory reveals the novel effect of site-selectivity of X-ray valence ionization caused by the excitation of the rotational degrees of freedom which is different for different ionization sites. Large recoil angular momentum related to the ejection of an electron from the light hydrogen atom results in a red shifted broad pedestal in the X-ray photoelectron spectrum of HCl.<br><p>QC 20131108</p>
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Ebbinghaus, Maximilian. "Stochastic modeling of intracellular processes : bidirectional transport and microtubule dynamics." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00592078.
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This thesis uses methods and models from non-equilibrium statistical physics to describe intracellular processes. Bidirectional microtubule-based transport within axons is modeled as a quasi-one-dimensional stochastic lattice gas with two particle species moving in opposite directions under mutual exclusion interaction. Generically occurring clusters of particles in current models for intracellular transport can be dissolved by additionally considering the dynamics of the transport lattice, i.e., the microtubule. An idealized model for the lattice dynamics is used to create a phase transition toward a homogenous state with efficient transport in both directions. In the thermodynamic limit, a steady state property of the dynamic lattice limits the maximal size of clusters. Lane formation mechanisms which are due to specific particle-particle interactions turn out to be very sensitive to the model assumptions. Furthermore, even if some particle-particle interaction is considered, taking the lattice dynamics into account almost always improves transport. Thus the lattice dynamics seems to be the key aspect in understanding how nature regulates intracellular traffic. The last part introduces a model for the dynamics of a microtubule which is limited in its growth by the cell boundary. The action of a rescue-enhancing protein which is added to the growing tip of a microtubule and then slowly dissociates leads to interesting aging effects which should be experimentally observable.
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Zoka, Assadi Masoud. "An investigation of cochlear dynamics in surgical and implantation processes." Thesis, Brunel University, 2011. http://bura.brunel.ac.uk/handle/2438/7966.
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The aim of this research is to improve the understanding of the impact on the cochlear dynamics corresponding to surgical tools, processes and hearing implants such that these can be designed more appropriately in the future. The results suggest that enhanced performance of implants can be achieved by optimisation of the location with respect to the cochlea and have shown that robotic surgical tools used to enable precise, simplified processes can reduce harm and offer other benefits. With an ageing population, and where exposure to noise on daily basis is increased rather than industrial settings, at least two factors of age and noise, will contribute to a greater incidence of hearing loss in the population in the future. In the research a mathematical model of the passive cochlea was produced to increase understanding of the sensitivity and behaviour of the fluid, structure and pressure transients within the cochlea. The investigation has been complemented by an innovative experimental technique developed to evaluate the dynamics in the cochlear fluids while maintaining the integrity of the cochlear structure. This technique builds on the success of the state-of-the-art surgical robotic micro-drill. The micro-drill enables removal of bone tissue to prepare a consistent aperture onto the endosteal membrane within the cochlea. This is known as preparing a ‘Third window’. In this technique the motion of the exposed endosteal membrane is treated as the diaphragm element of a pressure transducer and is measured using a Micro- Scanning Laser Vibrometer operating through a microscope. There are two principal outcomes of the research: First, the approach has enabled disturbances in the cochlea to be contrasted for different surgical techniques, which it is expected to allude preferential methods in future surgery in otology. In particular it was shown that when using the robotic micro-drill to create a cochleostomy that the disturbance amplitude reduces to 1% of that experienced when using conventional drilling. Secondly, an empirically derived frequency map of the cochlea has been produced to understand how the location of implants affects maximum power transmission over the required frequency band. This has also shown the feasibility of exciting the cochlea at a third window in order to amplify cochlear response.
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Quagraine, Kwesi Akumenyi. "Dynamics of co-behaviour of climate processes over Southern Africa." Doctoral thesis, Faculty of Science, 2021. http://hdl.handle.net/11427/33916.
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Large-scale climate processes such as El Niño-Southern Oscillation (ENSO), Antarctic Oscillation (AAO), and many others, play varying roles in regional climate variability across the world. While the role of singular processes have been explored in many studies, the combined influence of multiple large-scale processes has received far less attention. Key to this is the challenge of developing methodologies to support the analysis of multiple processes interacting in potentially non-linear ways (co-behaviour) in a particular region. This study details the development of such a methodology and demonstrates its utility in the analysis of the co-behaviour of largescale process interactions on regional precipitation and temperature variability over southern Africa. The study defines co-behaviour as the interaction of large-scale processes that may influence regional circulation leading to climate variability. A novel methodology which involves a combination of analysis techniques such as Self-Organizing Maps (SOM) and Principal Component Analysis (PCA) is developed to identify and quantify such co-behaviour which accommodates potentially non-linear interactions. This methodology is evaluated in the context of southern African regional climate using three key processes, namely ENSO, AAO and Inter-tropical Convergence Zone (ITCZ), and characterizations of regional circulation, and temperature and rainfall variability. Analysis of co-behaviour under observed conditions identifies results that concur with prior studies, in particular the dominant regional response to ENSO, but also establishes key examples of co-behaviour such as the role of the AAO in moderating and altering the regional response to ENSO which is important for understanding regional climate variability. Application of the approach to Global Climate Model (GCM) simulations of past climate reveals that while many GCMs are able to capture individual processes, in particular ENSO, they fail to adequately represent regional circulation variability and key observed co-behaviour. The study therefore clearly demonstrates the importance of co-behaviour in understanding regional climate variability as well as showing the usefulness of the new methodology in investigating co-behaviour. Finally, the new insights into evaluating model performance through the lens of core climate processes and their interaction provides a significant step forward in both model development and application for decision making.
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Bailey, Eva Machelor. "Processes Affecting Macroalgal-Seagrass Dynamics in the York River, Virginia." W&M ScholarWorks, 1998. https://scholarworks.wm.edu/etd/1539617969.
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Al-Rashed, Mohsen Hassan Jaber. "A study of reactive precipitation processes using computational fluid dynamics." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286284.
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Platt, John Daniel. "Dynamics and Materials Physics of Fault Rupture and Glacial Processes." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226054.
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This thesis focuses on two main topics, the physics governing how faults rapidly weaken during an earthquake and the thermal and mechanical structure of ice stream shear margins. The common theme linking these two projects is the desire to understand how the complicated interactions between stress and temperature control deformation and failure. All of the problems in this thesis are attacked using a combination of analytic and numerical methods, and the interplay between these two approaches provides a powerful way to understand the different physical balances that dominate in different regimes. We also use aspects of materials science to understand how the often complicated rheologies are controlled by underlying physical phenomena such as melting, phase transitions, diffusion, and dislocation motion. With regards to fault mechanics, we begin by showing how co-seismic weakening mechanisms driven by elevated pore fluid pressures lead to micron-scale strain localization during an earthquake. We solve for the localized zone thickness for a range of fault temperatures, test these predictions using numerical simulations, and show how the onset of localization accelerates fault weakening. Next we present the first solutions to account for thermal decomposition reactions during a dynamic rupture, showing that the activation of thermal decomposition may lead to a larger slip duration and total slip. Finally we present a new set of experiments studying flash heating of serpentinite, highlighting the dependence of friction on normal stress and the presence of gouge, and producing the first model to explain the hysteresis commonly observed in flash heating experiments. With regards to ice stream shear margins, we begin by extending the work of Perol and Rice [2011] to study the formation of temperate ice in shear margins, and quantify the total melt that may be generated within the shear margins. We conclude by investigating how the presence of such a channel alters the stress on and strength of the undeforming bed in the shear margin, showing that the transition from a deforming to an undeforming bed across a channel is stable when the water flux in the channel exceeds a critical value.
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Balaraman, Gouthaman S. "Theoretical study of atomic processes and dynamics in ultracold plasmas." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26522.
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Thesis (Ph.D)--Physics, Georgia Institute of Technology, 2009.<br>Committee Chair: M. R. Flannery; Committee Member: John Wood; Committee Member: Michael Schatz; Committee Member: Rigoberto Hernandez; Committee Member: Turgay Uzer. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Amiruddin. "The dynamics of subaqueous sediment gravity flows and redepositional processes." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/144399.
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Merlino, G. "STRUCTURE AND DYNAMICS OF MICROBIAL COMMUNITIES IN ANAEROBIC DIGESTION PROCESSES." Doctoral thesis, Università degli Studi di Milano, 2012. http://hdl.handle.net/2434/169990.
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Nowadays world energy needs rely mostly on fossil fuels (oil, coal and natural gas) which accounts for more than 80% of global energy production. Fossil fuels reserves are estimated to deplete in the next future. In this context, it arises the need to establish new renewable energetic sources. A well-established technology for bioenergy production in the form of biogas is anaerobic digestion (AD). This process involves a complex consortium of different functional groups of microbes which, degrading the organic matter, produce biogas composed mainly of methane and carbon dioxide. In the latest 10 years there has been renewed interest for energy production from biomass through AD because of its versatility and potentiality. So far, the control and performance of AD process has typically been performed working on operational parameters (such as T, pH, COD, loading rate, etc.). However, recent studies concerning the microbial consortia involved in this complex process have been developing with the final aim to get an exhaustive knowledge of microbiology of the process and how it correlates to the operation of the reactor in order to improve the digester performance making preventive action possible. the general aim of this PhD thesis was to investigate the microbiology of both batch and continuous, single and two-stage anaerobic systems. The goals were (i) to elucidate the structure of the microbial communities, (ii) to investigate the dynamics, interactions and responses of the key metabolic groups responsible for the degradation of substrates and (iii) to give valuable information on the correlation between structure and function inside the microbial consortiums.
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Sherborne, Neil. "Non-Markovian epidemic dynamics on networks." Thesis, University of Sussex, 2018. http://sro.sussex.ac.uk/id/eprint/79084/.
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The use of networks to model the spread of epidemics through structured populations is widespread. However, epidemics on networks lead to intractable exact systems with the need to coarse grain and focus on some average quantities. Often, the underlying stochastic processes are Markovian and so are the resulting mean-field models constructed as systems of ordinary differential equations (ODEs). However, the lack of memory (or memorylessness) does not accurately describe real disease dynamics. For instance, many epidemiological studies have shown that the true distribution of the infectious period is rather centred around its mean, whereas the memoryless assumption imposes an exponential distribution on the infectious period. Assumptions such as these greatly affect the predicted course of an epidemic and can lead to inaccurate predictions about disease spread. Such limitations of existing approaches to modelling epidemics on networks motivated my efforts to develop non-Markovian models which would be better suited to capture essential realistic features of disease dynamics. In the first part of my thesis I developed a pairwise, multi-stage SIR (susceptible-infected-recovered) model. Each infectious node goes through some K 2 N infectious stages, which for K > 1 means that the infectious period is gamma-distributed. Analysis of the model provided analytic expressions for the epidemic threshold and the expected final epidemic size. Using available epidemiological data on the infectious periods of various diseases, I demonstrated the importance of considering the shape of the infectious period distribution. The second part of the thesis expanded the framework of non-Markovian dynamics to networks with heterogeneous degree distributions with non-negligible levels of clustering. These properties are ubiquitous in many real-world networks and make model development and analysis much more challenging. To this end, I have derived and analysed a compact pairwise model with the number of equations being independent of the range of node degrees, and investigated the effects of clustering on epidemic dynamics. My thesis culminated with the third part where I explored the relationships between several different modelling methodologies, and derived an original non-Markovian Edge-Based Compartmental Model (EBCM) which allows both transmission and recovery to be arbitrary independent stochastic processes. The major result is a rigorous mathematical proof that the message passing (MP) model and the EBCM are equivalent, and thus, the EBCM is statistically exact on the ensemble of configuration model networks. From this consideration I derived a generalised pairwise-like model which I then used to build a model hierarchy, and to show that, given corresponding parameters and initial conditions, these models are identical to MP model or EBCM. In the final part of my thesis I considered the important problem of coupling epidemic dynamics with changes in network structure in response to the perceived risk of the epidemic. This was framed as a susceptible-infected-susceptible (SIS) model on an adaptive network, where susceptible nodes can disconnect from infected neighbours and, after some fixed time delay, connect to a random susceptible node that they are not yet connected to. This model assumes that nodes have perfect information on the state of all other nodes. Robust oscillations were found in a significant region of the parameter space, including an enclosed region known as an 'endemic bubble'. The major contribution of this work was to show that oscillations can occur in a wide region of the parameter space, this is in stark contrast with most previous research where oscillations were limited to a very narrow region of the parameter space. Any mathematical model is a simplification of reality where assumptions must be made. The models presented here show the importance of interrogating these assumptions to ensure that they are as realistic as possible while still being amenable to analysis.
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Bhopte, Siddharth. "Study of transport processes from macroscale to microscale." Diss., Online access via UMI:, 2009.
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Thesis (Ph. D.)--State University of New York at Binghamton, Thomas J. Watson School of Engineeering and Applied Science, Department of Mechanical Engineering, 2009.<br>Includes bibliographical references.
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Ismail, Atikah. "Fourier spectral methods for numerical modeling of ionospheric processes." Thesis, This resource online, 1994. http://scholar.lib.vt.edu/theses/available/etd-03142009-040454/.
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Baghery, Mehrdad. "Dynamics of Driven Quantum Systems:." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-232398.
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This thesis explores the possibility of using parallel algorithms to calculate the dynamics of driven quantum systems prevalent in atomic physics. In this process, new as well as existing algorithms are considered.
The thesis is split into three parts. In the first part an attempt is made to develop a new formalism of the time dependent Schroedinger equation (TDSE) in the hope that the new formalism could lead to a parallel algorithm. The TDSE is written as an eigenvalue problem, the ground state of which represents the solution to the original TDSE. Even though mathematically sound and correct, it turns out the ground state of this eigenvalue problem cannot be easily found numerically, rendering the original hope a false one.
In the second part we borrow a Bayesian global optimisation method from the machine learning community in an effort to find the optimum conditions in different systems quicker than textbook optimisation algorithms. This algorithm is specifically designed to find the optimum of expensive functions, and is used in this thesis to 1. maximise the electron yield of hydrogen, 2. maximise the asymmetry in the photo-electron angular distribution of hydrogen, 3. maximise the higher harmonic generation yield within a certain frequency range, 4. generate short pulses via combining higher harmonics generated by hydrogen.
In the last part, the phenomenon of dynamic interference (temporal equivalent of the double-slit experiment) is discussed. The necessary conditions are derived from first principles and it is shown where some of the previous analytical and numerical studies have gone wrong; it turns out the choice of gauge plays a crucial role. Furthermore, a number of different scenarios are presented where interference in the photo-electron spectrum is expected to occur.