Universität Stuttgart
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Item Open Access Thermodynamic inference in partially accessible Markov networks: a unifying perspective from transition-based waiting time distributions(2022) Meer, Jann van der; Ertel, Benjamin; Seifert, UdoThe inference of thermodynamic quantities from the description of an only partially accessible physical system is a central challenge in stochastic thermodynamics. A common approach is coarse-graining, which maps the dynamics of such a system to a reduced effective one. While coarse-graining states of the system into compound ones is a well-studied concept, recent evidence hints at a complementary description by considering observable transitions and waiting times. In this work, we consider waiting time distributions between two consecutive transitions of a partially observable Markov network. We formulate an entropy estimator using their ratios to quantify irreversibility. Depending on the complexity of the underlying network, we formulate criteria to infer whether the entropy estimator recovers the full physical entropy production or whether it just provides a lower bound that improves on established results. This conceptual approach, which is based on the irreversibility of underlying cycles, additionally enables us to derive estimators for the topology of the network, i.e., the presence of a hidden cycle, its number of states, and its driving affinity. Adopting an equivalent semi-Markov description, our results can be condensed into a fluctuation theorem for the corresponding semi-Markov process. This mathematical perspective provides a unifying framework for the entropy estimators considered here and established earlier ones. The crucial role of the correct version of time reversal helps to clarify a recent debate on the meaning of formal versus physical irreversibility. Extensive numerical calculations based on a direct evaluation of waiting time distributions illustrate our exact results and provide an estimate on the quality of the bounds for affinities of hidden cycles.Item Open Access Focus on stochastic thermodynamics(2016) Broeck, Christian Van den; Sasa, Shin-ichi; Seifert, UdoWe introduce the thirty papers collected in this ‘focus on’ issue. The contributions explore conceptual issues within and around stochastic thermodynamics, use this framework for the theoretical modeling and experimental investigation of specific systems, and provide further perspectives on and for this active field.Item Open Access Multiscale approaches to protein-mediated interactions between membranes : relating microscopic and macroscopic dynamics in radially growing adhesions(2015) Bihr, Timo; Seifert, Udo; Smith, Ana-SunčanaMacromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of deformable membranes, the diffusion of proteins and the molecular binding and unbinding. Because these stochastic processes couple over a multitude of time and length scales, theoretical modeling of membrane adhesion has been a major challenge. Here we present an effective Monte Carlo scheme within which the effects of the membrane are integrated into local rates for molecular recognition. The latter step in the Monte Carlo approach enables us to simulate the nucleation and growth of adhesion domains within a system of the size of a cell for tens of seconds without loss of accuracy, as shown by comparison to 106 times more expensive Langevin simulations. To perform this validation, the Langevin approach was augmented to simulate diffusion of proteins explicitly, together with reaction kinetics and membrane dynamics. We use the Monte Carlo scheme to gain deeper insight to the experimentally observed radial growth of micron sized adhesion domains, and connect the effective rate with which the domain is growing to the underlying microscopic events. We thus demonstrate that our technique yields detailed information about protein transport and complexation in membranes, which is a fundamental step toward understanding even more complex membrane interactions in the cellular context.Item Open Access Extreme fluctuations of active Brownian motion(2016) Pietzonka, Patrick; Kleinbeck, Kevin; Seifert, UdoIn active Brownian motion, an internal propulsion mechanism interacts with translational and rotational thermal noise and other internal fluctuations to produce directed motion. We derive the distribution of its extreme fluctuations and identify its universal properties using large deviation theory. The limits of slow and fast internal dynamics give rise to a kink-like and parabolic behavior of the corresponding rate functions, respectively. For dipolar Janus particles in two- and three-dimensions interacting with a field, we predict a novel symmetry akin to, but different from, the one related to entropy production. Measurements of these extreme fluctuations could thus be used to infer properties of the underlying, often hidden, network of states.Item Open Access Phase shift in periodically driven non-equilibrium systems : its identification and a bound(2022) Degünther, Julius; Koyuk, Timur; Seifert, UdoTime-dependently driven stochastic systems form a vast and manifold class of non-equilibrium systems used to model important applications on small length scales such as bit erasure protocols or microscopic heat engines. One property that unites all these quite different systems is some form of lag between the driving of the system and its response. For periodic steady states, we quantify this lag by introducing a generalized phase difference and prove a tight upper bound for it. In its most general version, this bound depends only on the relative speed of the driving.Item Open Access Waiting time distributions in hybrid models of motor-bead assays: a concept and tool for inference(2023) Ertel, Benjamin; Meer, Jann van der; Seifert, UdoItem Open Access Nonequilibrium sensing and its analogy to kinetic proofreading(2015) Hartich, David; Barato, Andre C.; Seifert, UdoFor a paradigmatic model of chemotaxis, we analyze the effect of how a nonzero affinity driving receptors out of equilibrium affects sensitivity. This affinity arises whenever changes in receptor activity involve adenosine triphosphate hydrolysis. The sensitivity integrated over a ligand concentration range is shown to be enhanced by the affinity, providing a measure of how much energy consumption improves sensing. With this integrated sensitivity we can establish an intriguing analogy between sensing with nonequilibrium receptors and kinetic proofreading: the increase in integrated sensitivity is equivalent to the decrease of the error in kinetic proofreading. The influence of the occupancy of the receptor on the phosphorylation and dephosphorylation reaction rates is shown to be crucial for the relation between integrated sensitivity and affinity. This influence can even lead to a regime where a nonzero affinity decreases the integrated sensitivity, which corresponds to anti-proofreading.Item Open Access Field-theoretic thermodynamic uncertainty relation : general formulation exemplified with the Kardar-Parisi-Zhang equation(2020) Niggemann, Oliver; Seifert, UdoWe propose 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 a field-theoretic thermodynamic uncertainty relation holds up to second order in a perturbation expansion with respect to a small effective coupling constant. The calculations show that the field-theoretic variant of the thermodynamic uncertainty relation is not saturated for the case of the Kardar-Parisi-Zhang equation due to an excess term stemming from its non-linearity.Item Open Access The two scaling regimes of the thermodynamic uncertainty relation for the KPZ-equation(2021) Niggemann, Oliver; Seifert, UdoWe investigate the thermodynamic uncertainty relation for the (1+1) dimensional Kardar-Parisi-Zhang (KPZ) equation on a finite spatial interval. In particular, we extend the results for small coupling strengths obtained previously to large values of the coupling parameter. It will be shown that, due to the scaling behavior of the KPZ equation, the thermodynamic uncertainty relation (TUR) product displays two distinct regimes which are separated by a critical value of an effective coupling parameter. The asymptotic behavior below and above the critical threshold is explored analytically. For small coupling, we determine this product perturbatively including the fourth order; for strong coupling we employ a dynamical renormalization group approach. Whereas the TUR product approaches a value of 5 in the weak coupling limit, it asymptotically displays a linear increase with the coupling parameter for strong couplings. The analytical results are then compared to direct numerical simulations of the KPZ equation showing convincing agreement.Item Open Access Thermodynamic cost of external control(2017) Barato, Andre C.; Seifert, UdoArtificial molecular machines are often driven by the periodic variation of an external parameter. This external control exerts work on the system of which a part can be extracted as output if the system runs against an applied load. Usually, the thermodynamic cost of the process that generates the external control is ignored. Here, we derive a refined second law for such small machines that include this cost, which is, for example, generated by free energy consumption of a chemical reaction that modifies the energy landscape for such a machine. In the limit of irreversible control, this refined second law becomes the standard one. Beyond this ideal limiting case, our analysis shows that due to a new entropic term unexpected regimes can occur: the control work can be smaller than the extracted work and the work required to generate the control can be smaller than this control work. Our general inequalities are illustrated by a paradigmatic three-state system.