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Subject: search.filters.subject.530Institute: search.filters.UBSInstitut.Institut für Theoretische Physik IIStart date: 2010End date: 2019Author: search.filters.author.Zimmermann, Eva

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    Dynamics and thermodynamics of molecular motor-cargo systems
    (2015) Zimmermann, Eva; Seifert, Udo (Prof. Dr.)
    This thesis is dedicated to the dynamics and thermodynamics of molecular motors. In particular, it focuses on the influence of a coupled probe particle on the properties of the motor protein. Molecular motors are enzymes that are able to convert chemical energy available from, e.g., ATP hydrolysis into mechanical motion. They are involved in a variety of important processes that account for cellular function like transport of organelles, cell division, muscle contraction and even ATP synthesis. Although molecular motors are microscopic objects of the size of several nanometers whose dynamics is strongly influenced by thermal fluctuations, they exhibit a surprisingly stable and efficient performance. Hence, understanding the structure and mode of operation is of great scientific relevance in the fields of physics, biology, chemistry and medicine. Experimental studies typically imply some kind of probe particle that is attached to the motor and serves as a sensor to visualize the motor motion and that allows to exert forces on the motor under investigation. Since these probe particles are often more than ten times larger than the motor itself, they can be expected to constitute a considerable hindrance to the motor and to severely influence its dynamics and thermodynamics. Inferring properties of the motor from experimental data is a delicate task since on the one hand, only the trajectory of the probe is directly accessible, while on the other hand any measurement results apply to the motor-probe complex rather than the motor itself. In the first place, it is often unclear which properties of the motor are influenced by the coupled probe and to what extent. Belonging to the class of mesoscopic biological systems, the dynamics of molecular motors is subject to thermal fluctuations. Furthermore, the motors operate under genuine nonequilibrium conditions. Hence, a theoretical description of these microscopic machines requires the consideration of fluctuations and nonequilibrium conditions, which is provided by the framework of stochastic dynamics and stochastic thermodynamics. In this thesis, we theoretically analyze the dynamics and energetics of a molecular motor coupled to a probe particle with regard to the effects caused by the presence of the probe. Our goal is to determine the influence of the probe particle on several properties of the motor dynamics and energetics and to identify features in the experimental data that are consequences of attaching a probe and do not belong to the motor itself. Furthermore, we provide a thermodynamically consistent procedure to simplify the theoretical description by mapping motor and probe to an effective motor particle. In order to investigate these effects we set up a generic model comprising two degrees of freedom representing motor and probe, respectively, that are coupled via an elastic linker. Results are obtained from Monte Carlo simulations of the system and from numerically solving the Fokker-Planck equation. In some cases, we also apply simplified models that can be solved analytically. We also compare our results to available experimental data.
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    Efficiencies of a molecular motor : a generic hybrid model applied to the F1-ATPase
    (2012) Zimmermann, Eva; Seifert, Udo
    In a single-molecule assay, the motion of a molecular motor is often inferred by measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic setup taking into account explicitly the elastic coupling between the probe and the motor. The combined dynamics consists of discrete steps of the motor and the continuous Brownian motion of the probe. Motivated by recent experiments on the F1-ATPase, we investigated three types of efficiencies both in simulations and in a Gaussian approximation. Overall, we obtained good quantitative agreement with the experimental data. In particular, we clarify the conditions under which one of these efficiencies becomes larger than 1.