xiv, 171 p. ; ill. (some col.) A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number. / Biological molecular motors, which use chemical energy from ATP hydrolysis to generate mechanical force, are involved in a variety of important mechanical processes in eukaryotic cells, such as intracellular transport, cell division and muscle contraction. These motors, which produce motion on the nanoscale, operate in the presence of substantial thermal noise. In this dissertation, two approaches are used to model the physics of nanoscale motors: (1) A theoretically established type of Brownian motor called the "flashing ratchet" is studied. This motor transports diffusive particles in a preferred direction. (2) A coarse-grained mechanical model for the biological molecular motor myosin-V is developed, and used to study the role of Brownian diffusion, and the interaction between chemical and mechanical degrees of freedom, in the transport mechanism of this motor. In chapter III, Brownian dynamics simulations and analytical calculations demonstrate that the average velocity of rigid chains of particles in a flashing ratchet reverses direction in response to changing the size of the chain or the temperature of the heat bath. Recent studies have introduced policies for "closed-loop" control of a flashing ratchet, in which the system is controlled based on information about its internal state (such as the positional distribution of particles). In chapter IV, the effect of time delay on the implementation of closed-loop control of a flashing ratchet is investigated. For a large ensemble, a well-chosen delay time improves the ratchet performance (increasing the velocity) by synchronizing into a quasi-stable mode that takes advantage of the semi-deterministic nature of the time development of average quantities for a large ensemble. I n chapter V, a coarse-grained mechanical model is presented for the transport mechanism of myosin-V, which walks along intracellular filaments. The model is well constrained by experimental data on the mechanical properties of myosin V and on the kinetic cycle. An experimentally motivated model for the intramolecular coordination of the motor's steps is proposed and tested. / Adviser: Heiner Linke

Rectification phenomena in two specific mesoscopic systems are reviewed. The phenomenon is called ratchet effect, and such systems are called ratchets. In this thesis, particularly a rocked quantum-dot ratchet, and a tunneling ratchet are considered. The origin of the name is explained in a brief historical background. Due to rectification, there is a net non-vanishing electronic current, whose direction can be reversed by changing rocking amplitude, the Fermi energy, or applying magnetic field to the devices (for the rocked ratchet), and tuning the temperature (for the tunneling ratchet). In the last part, a theoretical examination based on the Landauer-B&uuml / ttiker formalism of mesoscopic quantum transport is presented.

In this thesis, both experimental studies and numerical simulations of ultracold atoms in optical potentials are presented in a collection of nine scientific papers. In particular, noise-induced transport in dissipative optical lattices and superfluid properties of Bose-Einstein condensates have been studied. Noise is usually regarded as a complication to most systems and as something that needs to be minimized. However, in a series of experiments at Umeå University, noise has been shown to play a key role for laser-cooled cesium atoms trapped in dissipative optical lattices. By using a combination of two dissipative optical lattices, where the relative spatial phase between them can be controlled, a so-called Brownian motor can be realized, where energy can be extracted from the inherent noise. In the experiment, this energy is used to control the transport of the laser-cooled atoms in real time and along pre-designed paths. This thesis also presents a way to characterize this system in terms of energy conversion efficiency and coherence of the transport, which may allow for a more straightforward comparison with other systems that rely on noise rectification. In the studies, it is also shown that the noise triggers a downward drift due to gravity, even though the optical potential should support the atoms. Further investigation of this might help to understand the underlying principles of laser cooling, as well as showing that the system might be suitable as a flexible test bed for statistical physics. In close relation to the experimental system, two numerical simulations are also presented, one in which different ways to induce asymmetries between two periodic potentials are investigated, and one in which a proposal for detecting quantum walks is explored. In the second part of the thesis, a work from the Joint Quantum Institute is presented, where a long-lived persistent current in a toroidal Bose-Einstein condensate, held in an all-optical trap, is created. The critical velocity of the superflow is measured in the presence of a tunable barrier. The system can be seen as a first realization of an elementary closed-loop atom circuit. Finally a theoretical study of the crossover between one- and two-dimensional systems is presented, in particular the transition between a two-dimensional superfluid to a one-dimensional Mott insulator is investigated. / Medelst nio vetenskapliga artiklar presenteras i denna avhandling experimentella och teoretiska studier av ultrakalla atomer fångade i optiska potentialer. Framförallt har brusinducerade transporter och supraytande egenskaper hos Bose-Einstein-kondensat studerats.     För de flesta system betraktas brus som något negativt som bör minimeras, men i en serie experiment som redovisas i denna avhandling spelar bruset istället en avgörande positiv roll. I ett system där laserkylda atomer genom växelverkan med laserstrålar fångas i två individuella optiska kristallgitter, kan atomernas kollektiva rörelse styras genom att energi utvinns ur det inneboende bruset. I denna avhandling, genom att kontrollera de optiska potentialerna i realtid, visas att atomernas kollektiva rörelse kan styras längs förutbestämda banor med en så kallade Brownska motor. I ett annat experiment mäts verkningsgraden i omvandligen mellan brus och arbete, samt koherensen i atomtransporten. En sådan karakterisering gör att systemet blir enklare att jämföra med andra system som bygger på liknande principer. I avhandlingen presenteras också en studie där det visas att det inneboende bruset i systemet, tillsammans med en svag kraft, i detta fall från gravitation, kan skapa drifter trots att de optiska potentialerna borde vara tillräckligt djupa för att atomerna ska vara fångade. Denna upptäckt kan leda till ökad grundläggande kundskap om laserkylning. Dessutom visar det att systemet kan beskrivas med modeller från statistisk fysik. I relation till det experimentella systemet i Umeå redovisas även två teoretiska studier, en för två symmetriska periodiska potentialer och deras sätt att möjliggöra inducerade drifter med olika typ av asymmetrier, samt en annan för möjligheten att genomföra och detektera kvantvandringar.     I avhandlingen presenteras också ett experimentellt arbete utfört vid Joint Quantum Institute, där en långlivad ihållande ström i ett torusformat Bose-Einstein-kondensat har skapats i en optisk fälla. Den kritiska hastigheten på strömmen har mätts i närvaron av en ställbar optisk barriär. Detta system kan ses som en första realisation av en grundläggande atomkrets. Slutligen presenteras även en teoretisk studie av övergången mellan en- och tvådimensionella system, där fasövergången mellan superytande och Mottisolation studeras.

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

Physical systems far from thermo dynamic equilibrium present excitability and irreversibility. The excitability is responsible for the great sensitivity of these systems to external stimuli while the irreversibility is associated with energy dissipation. The thermal fluctuations, inevitable in any real system, arise due to the interaction between many particles of the system. For such systems one of the best approaches is given by the non-equilibrium Statistical Mechanics, since it is virtually impossible an individualized approach of the motion equations. Many works in the current literature use a Gaussian stochastic modeling (without correlations) to represent the fluctuations. However, there is a growing number of studies reporting the occurrence of correlated fluctuations, mainly related to biological systems. In this thesis we investigate the influence of non-Gaussian stochastic distribution on the properties for two representative excitable models. In the first model we study the influence of distribution on the neural dynamics through the stochastic resonance (SR) mechanism. In the second model we approach the ratchet effect (RE) on directed transport of particles. In both systems we use a non-Gaussian power-law distributed noise obtained through a random multiplicative process (RMP). This process allows a fine tuning of the asymptotic power-law decay exponent. The optimization conditions are reported. In particular, we show that the optimization conditions for resonance and directed transport in Brownian ratchets are reached for a finit decay exponent of the stochastic distribution that represents a Strong non-Gaussian character. As non-Gaussian fluctuations occur with great frequency in natural systems, we believe that the non-Gaussian character can optimize the efficiency on the stochastic transport mechanisms in micro and nanoscale. / Fundação de Amparo a Pesquisa do Estado de Alagoas / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Sistemas físicos fora do equilíbrio termo dinâmico apresentam excitabilidade e irreversibilidade. A excitabilidade é responsável pela grande sensibilidade desses sistemas a estímulos externos enquanto a irreversibilidade está asso ciada à dissipação de energia. As flutuações térmicas, inevitáveis em qualquer sistema real, surgem devido à interação entre as inúmeras partículas do meio. Para tais sistemas uma das melhores abordagens é dada pela Mecânica Estatística de não-equilíbrio, uma vez que é praticamente impossível uma abordagem individualizada das equações de movimento. Muitos trabalhos na literatura atual utilizam uma modelagem estocástica gaussiana (sem correlação) para representar as flutuações. No entanto, há um número crescente de trabalhos que relatam a ocorrência de flutuações correlacionadas, principalmente em sistemas biológicos. Nesta tese nós investigamos a influência da distribuição estocástica não-gaussiana sobre as propriedades de dois modelos excitáveis representativos. No primeiro, estudamos a influência da distribuição sobre a dinâmica neural através do mecanismo de ressonância estocástica (RE). No segundo, abordamos o mecanismo do efeito catraca (EC) sobre o transporte direcionado de partículas. Nos dois sistemas utilizamos um ruído colorido não-gaussiano com distribuição tipo lei de potência obtido através de um processo multiplicativo aleatório (PMA). Esse processo permite o ajuste no do expoente de decaimento assintótico da lei de potência. As condições de otimização são relatadas. Em particular, obtivemos que as condições de otimização para a ressonância e para o transporte direcionado em catracas brownianas são atingidas para um valor finito do expoente da distribuição estocástica que representa um caráter fortemente não-gaussiano. Como flutuações não-gaussianas o correm com muita frequência nos sistemas naturais, acreditamos que o caráter não-gaussiano pode otimizar a eficiência dos mecanismos estocásticos de transporte em micro e nanoescala.

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