Showing papers by "Udo Seifert published in 2019"
TL;DR: For a large class of nonequilibrium systems, thermodynamic notions like work, heat, and entropy production can be identified on the level of fluctuating dynamical trajectories as mentioned in this paper.
Abstract: For a large class of nonequilibrium systems, thermodynamic notions like work, heat, and, in particular, entropy production can be identified on the level of fluctuating dynamical trajectories. With...
158 citations
TL;DR: In this article, the authors derive a family of inequalities that relate entropy production with experimentally accessible data for the mean, its dependence on driving frequency, and the variance of a large class of observables.
Abstract: For periodically driven systems, we derive a family of inequalities that relate entropy production with experimentally accessible data for the mean, its dependence on driving frequency, and the variance of a large class of observables. With one of these relations, overall entropy production can be bounded by just observing the time spent in a set of states. Among further consequences, the thermodynamic efficiency both of isothermal cyclic engines like molecular motors under a periodic load and of cyclic heat engines can be bounded using experimental data without requiring knowledge of the specific interactions within the system. We illustrate these results for a driven three-level system and for a colloidal Stirling engine.
71 citations
TL;DR: In this paper, the optimal obstacle shape for such devices and benchmarks for the extraction of useful work from these systems are presented. But the optimal shape of the obstacle is not known.
Abstract: Asymmetric obstacles in active matter can act as novel type of engine. A new analysis reveals the optimal obstacle shape for such devices and benchmarks for the extraction of useful work from these systems.
69 citations
TL;DR: In this article, the authors generalize the thermodynamic uncertainty relation to periodically time-dependent systems and, relatedly, to a larger class of inherently timedependent current observables.
Abstract: The thermodynamic uncertainty relation expresses a universal trade-off between precision and entropy production, which applies in its original formulation to current observables in steady-state systems. We generalize this relation to periodically time-dependent systems and, relatedly, to a larger class of inherently time-dependent current observables. In the context of heat engines or molecular machines, our generalization applies not only to the work performed by constant driving forces, but also to the work performed while changing energy levels. The entropic term entering the generalized uncertainty relation is the sum of local rates of entropy production, which are modified by a factor that refers to an effective time-independent probability distribution. The conventional form of the thermodynamic uncertainty relation is recovered for a time-independently driven steady state and, additionally, in the limit of fast driving. We illustrate our results for a simple model of a heat engine with two energy levels.
64 citations
TL;DR: Numerical results for a three-dimensional variant and for further currents suggest that the existence of a universal lower bound on the product of entropy production and the fluctuations of any current depends crucially on the specific current.
Abstract: The thermodynamic uncertainty relation provides a universal lower bound on the product of entropy production and the fluctuations of any current. While proven for Markov dynamics on a discrete set of states and for overdamped Langevin dynamics, its status for underdamped dynamics is still open. We consider a two-dimensional harmonically confined charged particle in a magnetic field under the action of an external torque. We show analytically that, depending on the sign of the magnetic field, the thermodynamic uncertainty relation does not hold for the currents associated with work and heat. A strong magnetic field can effectively localize the particle with concomitant bounded fluctuations and low dissipation. Numerical results for a three-dimensional variant and for further currents suggest that the existence of such a bound depends crucially on the specific current.
55 citations
TL;DR: Surprisingly, this approach reveals that the interaction with the passive obstacle can mediate cooperativity between otherwise noninteracting active particles, which enhances the extracted power per active particle significantly.
Abstract: Because of its nonequilibrium character, active matter in a steady state can drive engines that autonomously deliver work against a constant mechanical force or torque. As a generic model for such an engine, we consider systems that contain one or several active components and a single passive one that is asymmetric in its geometrical shape or its interactions. Generally, one expects that such an asymmetry leads to a persistent, directed current in the passive component, which can be used for the extraction of work. We validate this expectation for a minimal model consisting of an active and a passive particle on a one-dimensional lattice. It leads us to identify thermodynamically consistent measures for the efficiency of the conversion of isotropic activity to directed work. For systems with continuous degrees of freedom, work cannot be extracted using a one-dimensional geometry under quite general conditions. In contrast, we put forward two-dimensional shapes of a movable passive obstacle that are best suited for the extraction of work, which we compare with analytical results for an idealised work-extraction mechanism. For a setting with many noninteracting active particles, we use a mean-field approach to calculate the power and the efficiency, which we validate by simulations. Surprisingly, this approach reveals that the interaction with the passive obstacle can mediate cooperativity between otherwise noninteracting active particles, which enhances the extracted power per active particle significantly.
22 citations
TL;DR: In this paper, it was shown that subharmonic response can persist for a long time in open systems with stochastic dynamics due to thermal fluctuations, even in networks with a small number of states.
Abstract: Subharmonic response is a well-known phenomenon in, e.g., deterministic nonlinear dynamical systems. We investigate the conditions under which such subharmonic oscillations can persist for a long time in open systems with stochastic dynamics due to thermal fluctuations. In contrast to stochastic autonomous systems in a stationary state, for which the number of coherent oscillations is fundamentally bounded by the number of states in the underlying network, we demonstrate that in periodically driven systems, subharmonic oscillations can in principle remain coherent forever, even in networks with a small number of states. We also show that, inter alia, the thermodynamic cost rises only logarithmically with the number of coherent oscillations in a model calculation and that the possible periods of the persistent subharmonic response grow linearly with the number of states. We argue that our results can be relevant for biochemical oscillations and for stochastic models of time crystals.
17 citations
TL;DR: This manuscript considers a single protein (elastic spring of a finite rest length) pinning a membrane modeled in the Monge gauge and explores static correlations of the free and the pinned membrane, as well as the membrane shape, showing that all three are mutually interdependent and have an identical long-range behavior characterized by the correlation length.
14 citations
TL;DR: In this article, a field-theoretic thermodynamic uncertainty relation is proposed for the one-dimensional Kardar-parisi-Zhang equation. But the relation is not applicable to the case of non-linear Langevin equations, and it is shown that the relation holds up to second order in perturbation expansion with respect to a small effective coupling constant.
Abstract: We introduce a field-theoretic thermodynamic uncertainty relation as an extension of the one derived so far for a Markovian dynamics on a discrete set of states and for overdamped Langevin equations. We first formulate a framework which describes quantities like current, entropy production and diffusivity in the case of a generic field theory. We will then apply this general setting to the one-dimensional Kardar-Parisi-Zhang equation, a paradigmatic example of a non-linear field-theoretic Langevin equation. In particular, we will treat the dimensionless Kardar-Parisi-Zhang equation with an effective coupling parameter measuring the strength of the non-linearity. It will be shown that the field-theoretic thermodynamic uncertainty relation holds up to second order in a perturbation expansion with respect to a small effective coupling constant.
8 citations
TL;DR: In this paper, the authors compare two network motifs, a single-species switch and an interlinked cascade that consists of two species coupled through positive and negative feedback loops, and find that interlinked cascades are closer to the ideal all-or-none switch and are more robust against fluctuating signals.
Abstract: GTPases regulate a wide range of cellular processes, such as intracellular vesicular transport, signal transduction and protein translation. These hydrolase enzymes operate as biochemical switches by toggling between an active guanosine triphosphate (GTP)-bound state and an inactive guanosine diphosphate (GDP)-bound state. We compare two network motifs, a single-species switch and an interlinked cascade that consists of two species coupled through positive and negative feedback loops. We find that interlinked cascades are closer to the ideal all-or-none switch and are more robust against fluctuating signals. While the single-species switch can only achieve bistability, interlinked cascades can be converted into oscillators by tuning the cofactor concentrations, which catalyse the activity of the cascade. These regimes can only be achieved with sufficient chemical driving provided by GTP hydrolysis. In this study, we present a thermodynamically consistent model that can achieve bistability and oscillations with the same feedback motif.
7 citations
TL;DR: In this article, the authors calculate the equilibrium power spectral density for an overdamped membrane pinned by an elastic, permanently attached spring subject to thermal excitations by considering the effects of the finite experimental resolution on the measured spectra, and extract the elasticity of the pinning from the experimentally measured spectrum.
TL;DR: In this paper, the authors conjecture a bound on the whole spectrum of these master matrices that constrains all eigenvalues in a fashion similar to the well known Perron-Frobenius theorem that is valid for any stochastic matrix.
Abstract: Affinity has proven to be a useful tool for quantifying the non-equilibrium character of time continuous Markov processes since it serves as a measure for the breaking of time reversal symmetry. It has recently been conjectured that the number of coherent oscillations, which is given by the ratio of imaginary and real part of the first non-trivial eigenvalue of the corresponding master matrix, is constrained by the maximum cycle affinity present in the network. In this paper, we conjecture a bound on the whole spectrum of these master matrices that constrains all eigenvalues in a fashion similar to the well known Perron-Frobenius theorem that is valid for any stochastic matrix. As in other studies that are based on affinity-dependent bounds, the limiting process that saturates the bound is given by the asymmetric random walk. For unicyclic networks, we prove that it is not possible to violate the bound by small perturbation of the asymmetric random walk and provide numerical evidence for its validity in randomly generated networks. The results are extended to multicyclic networks, backed up by numerical evidence provided by networks with randomly constructed topology and transition rates.
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TL;DR: This study presents a thermodynamically consistent model that can achieve bistability and oscillations with the same feedback motif and finds that interlinked cascades are closer to the ideal all-or-none switch and are more robust against fluctuating signals.
Abstract: GTPases regulate a wide range of cellular processes, such as intracellular vesicular transport, signal transduction, and protein translation. These hydrolase enzymes operate as biochemical switches by toggling between an active guanosine triphosphate (GTP)-bound state and an inactive guanosine diphosphate (GDP)-bound state. We compare two network motifs, a single-species switch and an interlinked cascade that consists of two species coupled through positive and negative feedback loops. We find that interlinked cascades are closer to the ideal all-or-none switch and are more robust against fluctuating signals. While the single-species switch can only achieve bistability, interlinked cascades can be converted into oscillators by tuning the cofactor concentrations, which catalyse the activity of the cascade. These regimes can only be achieved with sufficient chemical driving provided by GTP hydrolysis. In this study, we present a thermodynamically consistent model that can achieve bistability and oscillations with the same feedback motif.
TL;DR: In this paper, the authors compare two network motifs, a single-species switch and an interlinked cascade that consists of two species coupled through positive and negative feedback loops, and find that interlinked cascades are closer to the ideal all-or-none switch and are more robust against fluctuating signals.
Abstract: GTPases regulate a wide range of cellular processes, such as intracellular vesicular transport, signal transduction, and protein translation. These hydrolase enzymes operate as biochemical switches by toggling between an active guanosine triphosphate (GTP)-bound state and an inactive guanosine diphosphate (GDP)-bound state. We compare two network motifs, a single-species switch and an interlinked cascade that consists of two species coupled through positive and negative feedback loops. We find that interlinked cascades are closer to the ideal all-or-none switch and are more robust against fluctuating signals. While the single-species switch can only achieve bistability, interlinked cascades can be converted into oscillators by tuning the cofactor concentrations, which catalyse the activity of the cascade. These regimes can only be achieved with sufficient chemical driving provided by GTP hydrolysis. In this study, we present a thermodynamically consistent model that can achieve bistability and oscillations with the same feedback motif.
TL;DR: In this paper, the authors conjecture a bound on the whole spectrum of these master matrices that constrains all eigenvalues in a fashion similar to the well known Perron-Frobenius theorem that is valid for any stochastic matrix.
Abstract: Affinity has proven to be a useful tool for quantifying the non-equilibrium character of time continuous Markov processes since it serves as a measure for the breaking of time reversal symmetry. It has recently been conjectured that the number of coherent oscillations, which is given by the ratio of imaginary and real part of the first non-trivial eigenvalue of the corresponding master matrix, is constrained by the maximum cycle affinity present in the network. In this paper, we conjecture a bound on the whole spectrum of these master matrices that constrains all eigenvalues in a fashion similar to the well known Perron-Frobenius theorem that is valid for any stochastic matrix. As in other studies that are based on affinity-dependent bounds, the limiting process that saturates the bound is given by the asymmetric random walk. For unicyclic networks, we prove that it is not possible to violate the bound by small perturbation of the asymmetric random walk and provide numerical evidence for its validity in randomly generated networks. The results are extended to multicyclic networks, backed up by numerical evidence provided by networks with randomly constructed topology and transition rates.