Juntamente com o processo de mutação, a recombinação intragênica, vista como a troca recíproca de material genético entre genomas, é um dos principais fatores geradores da diversidade genética. De fato, os diversos mecanismos de recombinação existentes na natureza (sexo, por exemplo) são freqüentemente citados como invenções do processo de evolução via seleção natural para combater o efeito acumulativo de mutações deletéria, responsável pelo decréscimo gradual, mas contínuo, da adaptação (fitness) média de populações assexuadas de tamanho finito, num processo conhecido como catraca de Muller. Nesta dissertação, investigamos, através de simulações numéricas, como os mecanismos de recombinação afetam a velocidade da catraca de Muller em situações em que o efeito das mutações é multiplicativo, ou seja, o efeito deletério de uma nova mutação em um indivíduo independe das mutações anteriores. Trabalhamos com indivíduos haplóides de L genes que se reproduzem sexuadamente e estão sob a ação da seleção. Investigamos analiticamente o caso limite de população infinita e L = 2 genes, em que a catraca não atua. Para o caso específico de L = 1 onde, por construção, a recombinação não ocorre, derivamos a solução analítica da dinâmica evolutiva para qualquer tempo. De uma maneira geral, verificamos que a velocidade da catraca é retardada pelo acréscimo da taxa de recombinação. Em alguns dos casos estudados, essa velocidade tende a ser nula, indicando que o sexo pode evitar que populações sujeitas à ação de mutações deletérias sejam extintas. Nossos resultados numéricos também mostram que, como esperado, a movimentação da catraca tende a diminuir à medida que o tamanho da população aumenta. / Together with the mutation process, the intragenic recombination, viewed as the reciprocal exchange of genetic material between genomes, is one of the main factors responsible for genetic diversity. Indeed, the mechanisms of recombination existing in nature (e.g., sex) are frequently cited as inventions of the evolution process via natural selection to avoid the cumulative effect of deleterious mutations, responsible for the gradual but continuous decline in mean fitness of finite asexual populations, in a process known as Muller\'s ratchet. In this dissertation, we investigate, through numerical simulations, how the recombination mechanisms affect the rate of Muller\'s ratchet in situations in which the effect of mutations is multiplicative, that is, the deleterious effect of a new mutation in an individual does not depend on the mutations it already carries. We work with haploid individuals of L genes which reproduce sexually and are under the effect of selection and recombination. We analytically investigate the limit case of infinite population and L = 2 genes, where the ratchet does not operate. For the specific case in which L = 1 where, by construction, recombination doesn\'t occur, we derive the analytical solution of the evolution dynamics for any time. In general, we verify that the ratchet \'s rate is retarded by the increase in the recombination rate. In some of the cases we studied, this rate tends to be null, indicating that sex may provide means to avoid extinction of populations subjected to the action of deleterious mutations. Our numerical results also show, as expected, that the ratchet\'s rate tends to slow down according to the increase in population size.

Estudos sobre evolução têm sido desenvolvidos desde a publicação dos trabalhos de Charles Darwin sobre a origem das espécies pela seleção natural em 1859. Durante o século XX grandes avanços foram obtidos com a utilização de modelagens matemáticas e computacionais, pois com exceção de algumas espécies que podem ter sua evolução analisada in vivo, o tempo necessário para aquisição de dados é enorme e por este motivo o enfoque computacional passou a representar uma ferramenta essencial. Nesta tese são apresentados os conceitos básicos para se entender o processo evolutivo de populações assexuadas como mutação, seleção e relevos adaptativos, bem como os resultados numéricos sobre sua evolução através do processo conhecido como catraca de Muller, que baseia-se na perda estocástica da classe de indivíduos mais adaptados da população através das mutações adquiridas ao longo de sua linhagem. Neste trabalho foram estudadas diversas dinâmicas, como a de populações que estão sujeitas à passagens seriais com gargalo, onde observamos que a velocidade da catraca na não pára devido aos altos valores de epistase, enquanto que para populações com tamanho variável (crescimento e decrescimento exponencial) a catraca pára durante o período de crescimento até a população atingir o limite permitido pelo meio-ambiente, sendo que a partir deste ponto ela se comporta como no modelo de infinitos sítios tradicional. Por último, são apresentados os resultados de populações que interagem entre si em uma dinâmica presa-predador, onde o comportamento da catraca pode ser entendido com base nas dinâmicas das populações descritas anteriormente. Um outro problema abordado nesta tese é o da utilização de medidas da topologia de árvores genealógicas para verificar a presença da seleção na evolução de uma população. Apesar dos comprimentos dos ramos das árvores apresentarem alterações quando comparados ao caso neutro, observamos que os testes estatísticos utilizados não são suficientes para inferir o efeito da seleção em populações reais. / Studies about evolution have been developed since Charles Darwin\'s publications about the Origin of species and Natural Selection in 1859. During the XX century major developments were achieved through mathematical and computational modeling, since only few number of species that their evolution can be studied in vivo, once that the time scale involed for data acquisition procedure is considerable, and for this reason the computational approach become an important tool in this study. In this thesis are presented the basic concepts to understand the process of evolution in a population as mutation, selection and adaptive landscapes, in addition some numerical results about the evolution of an asexual population using the process known as Muller\'s ratchet, that can be characterized by the stochastic loss of the most fitted class of individuals through mutations that are acquired in their lineages. During this work several dynamics were studied, likewise the populations under serial bottleneck passages, where we observed that the velocity of the ratchet never stops for high epistatic coefficients, while in population whose size can varies (increasing or decreasing exponentially) the ratchet halts during population\'s increasing until these individuals do not reach the maximum number permitted, and after this point this population behaves like the traditional infinite genome size model. At last, we show the results of populations that can interact between themselves in a predator-prey dynamics, where the behaviour of the ratchet can be understood in the previous dynamics. Another problem that was studied in this thesis is related with several topology measures of genealogical trees in order to verify the selection in a population evolution. Despite branch\'s length of the trees changed due to the selection, we could see that the statistical tests used do not be sufficient to infer the effect of selection under real populations.

Submitted by Kamila Costa (kamilavasconceloscosta@gmail.com) on 2015-06-19T19:03:38Z No. of bitstreams: 1 Dissertação-Carlos F de O Mendes.pdf: 2879258 bytes, checksum: f17f29894c03ef3d86d4a3566328988e (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2015-07-06T19:16:17Z (GMT) No. of bitstreams: 1 Dissertação-Carlos F de O Mendes.pdf: 2879258 bytes, checksum: f17f29894c03ef3d86d4a3566328988e (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2015-07-06T19:20:01Z (GMT) No. of bitstreams: 1 Dissertação-Carlos F de O Mendes.pdf: 2879258 bytes, checksum: f17f29894c03ef3d86d4a3566328988e (MD5) / Made available in DSpace on 2015-07-06T19:20:01Z (GMT). No. of bitstreams: 1 Dissertação-Carlos F de O Mendes.pdf: 2879258 bytes, checksum: f17f29894c03ef3d86d4a3566328988e (MD5) Previous issue date: 2014-12-09 / CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico / In this work we consider the dynamical aspect of open quantum systems where a particle is subject to energy exchange with the environment. The environment (bath) consists of a finite number N of harmonic oscillators (HOs), characterizing a structured bath, for which a non-Markovian behavior is expected. We determine the numerical solution of the stochastic Schrödinger equation for a particle coupled to the bath. We study two different situations for the system’s particle: the harmonic potential and the ratchet potential. In the limit N → ¥ the bath is assumed to have an ohmic, sub-ohmic, and super-ohmic spectral density. In the case of the harmonic potential, for low values of N we observe an energy exchange between system and bath indefinitely in time, while for intermediate values of N is observed a decay in two time regimes: exponential for short times and power law for larger times. In the case of the ratchet potential, we observe that the energy returns to the systemeven for intermediate values of N. Wave packets are used to determine the evolution of the particle in the system potential. / Neste trabalho consideramos o aspecto dinâmico de sistemas quânticos abertos onde uma partícula fica sujeita a trocas de energia com o ambiente. O ambiente (banho) é composto de um número finito N de osciladores harmônicos (HOs), caracterizando um banho estruturado, para o qual um comportamento não-Markoviano é esperado. Determinamos a solução numérica da equação de Schrödinger estocástica para uma partícula acoplada ao banho. Estudamos duas situações distintas para o sistema de partícula: o potencial harmônico e o potencial de catraca. No limite N → ¥ o banho é assumido ter um espectro de densidade ôhmico, sub-ôhmico e super-ôhmico. No caso do potencial harmônico, para baixos valores de N observamos uma troca de energia entre sistema e banho indefinidamente no tempo, enquanto que para valores intermediários de N observa-se decaimento em dois regimes de tempo: exponencial para baixos valores de tempo e lei de potência para valores mais altos de tempo. No caso do potencial de catraca, observamos que a energia volta para o sistema até para valores intermediários de N. Pacotes de ondas são usadas para determinar a evolução da partícula nos potenciais do sistema.

Plusieurs mécanismes biologiques utilisent la polymérisation des filaments d'actine comme moteur mécanique. L'énergie chimique libérée à l'addition d'un monomère dans le filament est convertie en travail mécanique et une force est générée. Les filaments ainsi formés s'organisent grâce à des protéines liant l'actine et forment des structures qui diffèrent par leurs propriétés mécaniques et élastiques mais aussi de leurs fonctions dans les différents processus biologiques. Notre système expérimental permet d'étudier le lien entre les propriétés mécaniques et les mécanismes à l'origine de la production de la force. La polymérisation des filaments est directement initiée sur la surface de particules magnétiques. En présence d'un champ magnétique, ces dernières s'organisent en chaîne par des interactions dipôle-dipôle, et une force magnétique compressive est induite sur les filaments qui polymérisent. La polymérisation écartent les particules au cours du temps et en fonction de la force appliquée, la vitesse d'écartement des particules est ralentie. En suivant l'évolution de la distance entre particules, nous détaillons la relation force-vitesse et les propriétés mécaniques des filaments.

This study investigates the determinants and effects of currency and asset substitution in Turkey using quarterly data from 1987:1 to 2002:4. The empirical results from the application of Johansen procedure to a four-variable system containing currency-asset substitution proxy (M2Y/M2)), real income, real exchange rate, and ratchet effect proxy (past peak values of the depreciation of the real exchange rate) suggest the presence of a single cointegration vector among the variables. The results further suggest the endogeneity of the degree of currency substitution for the parameters of the cointegration vector. According to the theory consistent and data-acceptable long-run relationship between the variables, there is a strong ratchet (hysteresis) effect in currency-asset substitution in Turkey. The study contains also the policy implications of both currency substitution and the ratchet effect arising from real exchange rate change shocks in the Turkish economy.

Holding educators more accountable for the academic achievement of their students has been a central feature of recent education reforms. In several prominent instances, accountability schemes have set pecuniary performance targets that condition on prior scores as a means of controlling for student heterogeneity. Yet doing so introduces a potential dynamic distortion in incentives: teachers may be less responsive to the reform today in an effort to avoid more onerous targets in future — an instance of the so-called `ratchet effect.' The main chapters of this thesis consider possible dynamic distortions from three distinct but related vantage points. Chapter 2 builds a theoretical foundation for understanding the origin of ratchet effects in an educational context. Given an environment where school-level targets depend on student prior scores, I show that such dynamic gaming behaviour depends crucially on variation in the grade horizon of students, with teachers distorting their effort less when their decision affects fewer future scores within the same school. Chapter 3 analyzes the ratchet effect from an empirical perspective. Making use of rich educational panel data from North Carolina, I exploit variation in the grade span of schools to identify ratchet effects, finding compelling evidence of dynamic distortions using a difference-in-differences approach. I then directly estimate the structural parameters of the corresponding model, allowing for complementarities in production between teacher effort and student ability. Using these estimates, the grade five score in K-5 schools would be about 1.25 standard deviations lower under a counterfactual setting without any accountability scheme and 4.6% of a standard deviation higher if ratchet effects were eliminated via a prescribed reduction in each school's incentive target. Chapter 4 explores a potentially important class of mechanisms through which the identified dynamic effects might arise. In particular, school principals may re-allocate teachers across classrooms differentially by grade. By examining the yearly change in teacher assignments to tested subjects, I find evidence that principals re-sort higher quality teachers to higher grades and focus more costly re-sorting on lower grades in response to the reform, which is consistent with the overarching dynamic objective and results of the prior chapter.

Holding educators more accountable for the academic achievement of their students has been a central feature of recent education reforms. In several prominent instances, accountability schemes have set pecuniary performance targets that condition on prior scores as a means of controlling for student heterogeneity. Yet doing so introduces a potential dynamic distortion in incentives: teachers may be less responsive to the reform today in an effort to avoid more onerous targets in future — an instance of the so-called `ratchet effect.' The main chapters of this thesis consider possible dynamic distortions from three distinct but related vantage points. Chapter 2 builds a theoretical foundation for understanding the origin of ratchet effects in an educational context. Given an environment where school-level targets depend on student prior scores, I show that such dynamic gaming behaviour depends crucially on variation in the grade horizon of students, with teachers distorting their effort less when their decision affects fewer future scores within the same school. Chapter 3 analyzes the ratchet effect from an empirical perspective. Making use of rich educational panel data from North Carolina, I exploit variation in the grade span of schools to identify ratchet effects, finding compelling evidence of dynamic distortions using a difference-in-differences approach. I then directly estimate the structural parameters of the corresponding model, allowing for complementarities in production between teacher effort and student ability. Using these estimates, the grade five score in K-5 schools would be about 1.25 standard deviations lower under a counterfactual setting without any accountability scheme and 4.6% of a standard deviation higher if ratchet effects were eliminated via a prescribed reduction in each school's incentive target. Chapter 4 explores a potentially important class of mechanisms through which the identified dynamic effects might arise. In particular, school principals may re-allocate teachers across classrooms differentially by grade. By examining the yearly change in teacher assignments to tested subjects, I find evidence that principals re-sort higher quality teachers to higher grades and focus more costly re-sorting on lower grades in response to the reform, which is consistent with the overarching dynamic objective and results of the prior chapter.

xii, 112 p. : ill. (some col.) / Biological molecular motors exist in an interesting regime of physics where momentum is unimportant and diffusive motion is large. While only exerting small forces, these motors still manage to achieve directed motion and do work. Brownian motors induce directed motion of diffusive particles and are used as models for biological and artificial molecular motors. A flashing ratchet is a Brownian motor that rectifies thermal fluctuations of diffusive particles through the use of a time-dependent, periodic, and asymmetric potential. It has been predicted that a feedback-controlled flashing ratchet has a center of mass speed as much as one order of magnitude larger than the optimal periodically flashing ratchet. We have successfully implemented the first experimental feedback ratchet and observed the predicted order of magnitude increase in velocity. We experimentally compare two feedback algorithms for small particle numbers and find good agreement with Langevin dynamics simulations. We also find that existing algorithms can be improved to be more tolerant to feedback delay times. This experiment was implemented by a scanning line optical trap system. In a bottom-up approach to understanding molecular motors, a synthetic protein-based molecular motor, the "tumbleweed", is being designed and constructed. This design uses three ligand dependent DNA repressor proteins to rectify diffusive motion of the construct along a DNA track. To predict the behavior of this artificial motor one needs to understand the binding and unbinding kinetics of the repressor proteins at a single-molecule level. An assay, similar to tethered particle motions assays, has been developed to measure the unbinding rates of these three DNA repressor proteins. In this assay the repressor is immobilized to a surface in a microchamber. Long DNA with the correct recognition sequence for one of the repressors is attached to a microsphere. As the DNA-microsphere construct diffuses through the microchamber it will sometimes bind to the repressor protein. Using brightfield microscopy and a CCD camera the diffusive motion of the microsphere can be characterized and bound and unbound states can be differentiated. This method is tested for feasibility and shown to have sufficient resolution to measure the unbinding rates of the repressor proteins. / Committee in charge: Dr. Raghu Parthasarathy, Chair; Dr. Heiner Linke, Research Advisor; Dr. Dan Steck; Dr. John Toner; Dr. Brad Nolan

xii, 122 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / Biological molecular motors achieve directed motion and perform work in an environment dominated by thermal noise and in most cases incorporate thermally driven motion into the motor process. Inspired by bio-molecular motors, many other motor systems that incorporate thermal motion have been developed and studied. These motors are broadly referred to as Brownian motors. This dissertation presents simulation studies of two particular Brownian motors, the feedback-controlled flashing ratchet and an artificial molecular motor concept, the results of which not only drive experimental considerations but also illuminate physical behaviors that may be applicable to other Brownian motors. A flashing ratchet rectifies the motion of diffusive particles using a time dependent, asymmetric potential energy landscape, and the transport speed of the ratchet can be increased if information about the particle distribution is incorporated as feedback in the time dependency of the landscape. Using a Langevin Dynamics simulation, we compare two implementations of feedback control, a discrete algorithm and a continuous algorithm, and find that the discrete algorithm is less sensitive to fluctuations in the particle distribution. We also model an experimental system with time delay and find that the continuous algorithm can be improved by adjusting the feedback criteria to react to the expected state of the system after the delay time rather than the real-time state of the system. Motivated by the desire to understand bio-molecular linear stepping motors, we present a bottom-up approach of designing an artificial molecular motor. We develop a coarse-grained Molecular Dynamics model that is used to understand physical contributions to the diffusive stepping time of the motor and discover that partially reducing the diffusional space from 3D to 1D can dramatically increase motor speed. We also develop a stochastic model based on the classical Master equation for the system and explore the sensitivity of the motor to currently undetermined experimental parameters. We find that a reduced diffusional stepping time is critical to maintain motor attachment for many successive steps and explore an experimental design effect that leads to motor misstepping. / Committee in charge: Stephen Kevan, Chairperson, Physics; Heiner Linke, Member, Physics; John Toner, Member, Physics; Raghuveer Parthasarathy, Member, Physics; Marina Guenza, Outside Member, Chemistry

CISNE JÚNIOR, Roberto Lima da Costa. Transporte de partículas em canais catraca. 2009. 66 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2009. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-06-16T21:32:32Z No. of bitstreams: 1 2009_dis_rlccisnejunior.pdf: 1393454 bytes, checksum: 62607b402f92579c7e8e6941eb686ea3 (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-06-18T18:19:21Z (GMT) No. of bitstreams: 1 2009_dis_rlccisnejunior.pdf: 1393454 bytes, checksum: 62607b402f92579c7e8e6941eb686ea3 (MD5) / Made available in DSpace on 2015-06-18T18:19:21Z (GMT). No. of bitstreams: 1 2009_dis_rlccisnejunior.pdf: 1393454 bytes, checksum: 62607b402f92579c7e8e6941eb686ea3 (MD5) Previous issue date: 2009 / In this work we study the transport process of fluid flow and mass through channels that are characterized by periodic structures, namely ratchet channels. In the first part of this work, we approach a brief discussion on the characteristics of the flow in smooth channels, since they have simple analytical solution, and may help us understand the fluid flow through more complex channels. Then we study the fluid flow in ratchet channels, and we compare the results obtained for the fluid flow through smooth and ratchet channels, observing some similarities and differences between both of them. We show that the nature of the geometry of the ratchet channel adds a degree of complexity to the problem of the fluid flow, that affects the properties of the velocity and pressure fields. Moreover, we inquire into another aspect of the transport process, namely the transport of massive particle dragged by a fluid that flows in the interior of the ratchet channels previously mentioned. We show some results that indicate a certain typical similatiry between ratchet and smooth channels. However, the ratchet channels possess a structure that allows the break of symmetry in relation of the two only allowed directions of flow. In this way, the nature of the particle transport process can be affected by this break of simmetry. The aim of this work is to analyze the dynamics of particle transport into a ratched channel and determine which mechanisms play a fundamental role in this process. / Neste trabalho trataremos do transporte de fluido e partículas no interior de canais caracterizados por estruturas periódicas que lembram dentes de catraca, desta forma chamamos de canais catraca. Para tal tarefa iniciaremos com uma breve discussão sobre as características do escoamento em canais lisos, visto que os mesmos possuem solução analítica simples, e poderão nos ajudar a compreender o escoamento em canais mais complexos. Em seguida faremos o estudo do escoamento em canais catraca, e faremos a comparação entre os resultados obtidos para o escoamento em canais lisos e em canais catraca, mostrando algumas semelhanças e diferenças. Mostramos que a natureza da geometria do canal catraca adiciona um grau de complexidade ao problema do escoamento, refletindo-se nas propriedades dos campos de velocidade e pressão. Em seguida, faremos o estudo do comportamento do transporte de partículas com massa arrastadas por um fluido escoando no interior dos canais catraca, mostrando alguns resultados que indicam uma certa característica típica de canais lisos. Porém, devido os canais catracas possuírem uma estrutura que permite a quebra de simetria em relação aos dois únicos sentidos de fluxo permitidos, poderão aparecer mudanças no comportamento tanto do transporte de fluido como do transporte de partículas. Como ponto principal deste trabalho, analisaremos como surgem estas diferenças e quais os mecanismos desempenham papel fundamental para que isto aconteça.