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Various experimental techniques have been advanced in recent years to measure non-equilibrium energy transformations on the microscopic scale of single molecules. In general, the systems studied in the corresponding experiments are exposed to strong thermal fluctuations and thus the relevant energetic variables such as work and heat become stochastic. This thesis addresses challenging theoretical problems in this active field of current research: 1) Exact analytical solutions of work and heat distributions for isothermal non-equilibrium processes in suitable models are obtained; 2) Corresponding solutions for cyclic processes involving two different heat reservoirs are found; 3) Optimization of periodic driving protocols for such cyclic processes with respect to maximal output power, efficiency and minimal power fluctuations is studied. The exact solutions for work and heat distributions provide a reference for theoretical investigations of more complicated models, giving insight into the structure of the tail of work distributions and serving as valuable test cases for simulations of the underlying stochastic processes.
Progress of thermodynamics has been stimulated by the findings of a variety of fields of science and technology. The principles of thermodynamics are so general that the application is widespread to such fields as solid state physics, chemistry, biology, astronomical science, materials science, and chemical engineering. The contents of this book should be of help to many scientists and engineers.
This book explains the state-of-the-art algorithms used to simulate biological dynamics. Each technique is theoretically introduced and applied to a set of modeling cases. Starting from basic simulation algorithms, the book also introduces more advanced techniques that support delays, diffusion in space, or that are based on hybrid simulation strategies. This is a valuable self-contained resource for graduate students and practitioners in computer science, biology and bioinformatics. An appendix covers the mathematical background, and the authors include further reading sections in each chapter.
The nonequilibrium behavior of nanoscopic and biological systems, which are typically strongly fluctuating, is a major focus of current research. Lately, much progress has been made in understanding such systems from a thermodynamic perspective. However, new theoretical challenges emerge when the fluctuating system is additionally subject to time delay, e.g. due to the presence of feedback loops. This thesis advances this young and vibrant research field in several directions. The first main contribution concerns the probabilistic description of time-delayed systems; e.g. by introducing a versatile approximation scheme for nonlinear delay systems. Second, it reveals that delay can induce intriguing thermodynamic properties such as anomalous (reversed) heat flow. More generally, the thesis shows how to treat the thermodynamics of non-Markovian systems by introducing auxiliary variables. It turns out that delayed feedback is inextricably linked to nonreciprocal coupling, information flow, and to net energy input on the fluctuating level.
This thesis both broadens and deepens our understanding of the Brownian world. It addresses new problems in diffusion theory that have recently attracted considerable attention, both from the side of nanotechnology and from the viewpoint of pure academic research. The author focusses on the difussion of interacting particles in restricted geometries and under externally controlled forces. These geometries serve, for example, to model ion transport through narrow channels in cell membranes or a Brownian particle diffusing in an optical trap, now a paradigm for both theory and experiment. The work is exceptional in obtaining explicit analytically formulated answers to such realistic, experimentally relevant questions. At the same time, with its detailed exposition of the problems and a complete set of references, it presents a clear and broadly accessible introduction to the domain. Many of the problem settings and the corresponding exact asymptotic laws are completely new in diffusion theory.