Author

# Udo Seifert

Other affiliations: Forschungszentrum Jülich, Technische Universität München, University of California, Santa Barbara ...read more

Bio: Udo Seifert is an academic researcher from University of Stuttgart. The author has contributed to research in topic(s): Entropy production & Fluctuation theorem. The author has an hindex of 74, co-authored 308 publication(s) receiving 22363 citation(s). Previous affiliations of Udo Seifert include Forschungszentrum Jülich & Technische Universität München.

##### Papers published on a yearly basis

##### Papers

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TL;DR: Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production.

Abstract: Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (Some figures may appear in colour only in the online journal) This article was invited by Erwin Frey.

2,273 citations

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TL;DR: In this article, the authors describe the systematic physical theory developed to understand the static and dynamic aspects of membrane and vesicle configurations, and the preferred shapes arise from a competition between curvature energy which derives from the bending elasticity of the membrane, geometrical constraints such as fixed surface area and fixed enclosed volume, and a signature of the bilayer aspect.

Abstract: Vesicles consisting of a bilayer membrane of amphiphilic lipid molecules are remarkably flexible surfaces that show an amazing variety of shapes of different symmetry and topology. Owing to the fluidity of the membrane, shape transitions such as budding can be induced by temperature changes or the action of optical tweezers. Thermally excited shape fluctuations are both strong and slow enough to be visible by video microscopy. Depending on the physical conditions, vesicles adhere to and unbind from each other or a substrate. This article describes the systematic physical theory developed to understand the static and dynamic aspects of membrane and vesicle configurations. The preferred shapes arise from a competition between curvature energy, which derives from the bending elasticity of the membrane, geometrical constraints such as fixed surface area and fixed enclosed volume, and a signature of the bilayer aspect. These shapes of lowest energy are arranged into phase diagrams, which separate regi...

1,456 citations

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TL;DR: The integrated sum of both Delatas(tot) is shown to obey a fluctuation theorem (exp([-Deltas( tot) = 1 for arbitrary initial conditions and arbitrary time-dependent driving over a finite time interval)).

Abstract: For stochastic nonequilibrium dynamics like a Langevin equation for a colloidal particle or a master equation for discrete states, entropy production along a single trajectory is studied. It involves both genuine particle entropy and entropy production in the surrounding medium. The integrated sum of both $\ensuremath{\Delta}{s}_{\mathrm{tot}}$ is shown to obey a fluctuation theorem $⟨\mathrm{exp} [\ensuremath{-}\ensuremath{\Delta}{s}_{\mathrm{tot}}]⟩=1$ for arbitrary initial conditions and arbitrary time-dependent driving over a finite time interval.

1,105 citations

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TL;DR: Vesicle shapes of low energy are studied for two variants of a continuum model for the bending energy of the bilayer, which lead to different predictions for typical trajectories, such as budding trajectories or oblate-stomatocyte transitions.

Abstract: Vesicle shapes of low energy are studied for two variants of a continuum model for the bending energy of the bilayer: (i) the spontaneous-curvature model and (ii) the bilayer-coupling model, in which an additional constraint for the area difference of the two monolayers is imposed. We systematically investigate four branches of axisymmetric shapes: (i) the prolate-dumbbell shapes; (ii) the pear-shaped vesicles, which are intimately related to budding; (iii) the oblate-discocyte shapes; and (iv) the stomatocytes. These branches end up at limit shapes where either the membrane self-intersects or two (or more) shapes are connected by an infinitesimally narrow neck. The latter limit shape requires a certain condition between the curvatures of the adjacent shape and the spontaneous curvature. For both models, the phase diagram is determined, which is given by the shape of lowest bending energy for a given volume-to-area ratio and a given spontaneous curvature or area difference, respectively. The transitions between different shapes are continuous for the bilayer-coupling model, while most of the transitions are discontinuous in the spontaneous-curvature model. We introduce trajectories into these phase diagrams that correspond to a change in temperature and osmotic conditions. For the bilayer-coupling model, we find extreme sensitivity to an asymmetry in the monolayer expansivity. Both models lead to different predictions for typical trajectories, such as budding trajectories or oblate-stomatocyte transitions. Our study thus should provide the basis for an experimental test of both variants of the curvature model.

794 citations

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TL;DR: It is shown quite generally that, in a steady state, the dispersion of observables, like the number of consumed or produced molecules or thenumber of steps of a motor, is constrained by the thermodynamic cost of generating it.

Abstract: Biomolecular systems like molecular motors or pumps, transcription and translation machinery, and other enzymatic reactions, can be described as Markov processes on a suitable network. We show quite generally that, in a steady state, the dispersion of observables, like the number of consumed or produced molecules or the number of steps of a motor, is constrained by the thermodynamic cost of generating it. An uncertainty $\ensuremath{\epsilon}$ requires at least a cost of $2{k}_{B}T/{\ensuremath{\epsilon}}^{2}$ independent of the time required to generate the output.

471 citations

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28,684 citations

28 Jul 2005

TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

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TL;DR: In this paper, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry.

Abstract: The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

4,818 citations

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TL;DR: Van Kampen as mentioned in this paper provides an extensive graduate-level introduction which is clear, cautious, interesting and readable, and could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes.

Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

3,620 citations

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TL;DR: In this paper, the authors describe the rules of the ring, the ring population, and the need to get off the ring in order to measure the movement of a cyclic clock.

Abstract: 1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

3,308 citations