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Udo Seifert

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


Papers
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TL;DR: This work shows that biochemical oscillations emerge through a generic nonequilibrium phase transition, with a characteristic qualitative behavior at criticality, and argues that the number of coherent oscillations is more appropriate to quantify the precision of biochemical oscillation.
Abstract: Biochemical oscillations are ubiquitous in living organisms. In an autonomous system, not influenced by an external signal, they can only occur out of equilibrium. We show that they emerge through a generic nonequilibrium phase transition, with a characteristic qualitative behavior at criticality. The control parameter is the thermodynamic force which must be above a certain threshold for the onset of biochemical oscillations. This critical behavior is characterized by the thermodynamic flux associated with the thermodynamic force, its diffusion coefficient, and the stationary distribution of the oscillating chemical species. We discuss metrics for the precision of biochemical oscillations by comparing two observables, the Fano factor associated with the thermodynamic flux and the number of coherent oscillations. Since the Fano factor can be small even when there are no biochemical oscillations, we argue that the number of coherent oscillations is more appropriate to quantify the precision of biochemical oscillations. Our results are obtained with three thermodynamically consistent versions of known models: the Brusselator, the activator-inhibitor model, and a model for KaiC oscillations.

42 citations

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TL;DR: In this paper, the viscous and non-viscous modes of a free bilayer membrane are discussed, taking into account the coupling between bending and the local density of the two monolayers.

41 citations

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TL;DR: This study demonstrates the utility of optical stretching, which is easily combined with microfluidic delivery, for the future serial, high-throughput study of the mechanical and thermodynamic properties of phospholipid vesicles.
Abstract: Phospholipid vesicles are common model systems for cell membranes. Important aspects of the membrane function relate to its mechanical properties. Here we have investigated the deformation behaviour of phospholipid vesicles in a dual-beam laser trap, also called an optical stretcher. This study explicitly makes use of the inherent heating present in such traps to investigate the dependence of vesicle deformation on temperature. By using lasers with different wavelengths, optically induced mechanical stresses and temperature increase can be tuned fairly independently with a single setup. The phase transition temperature of vesicles can be clearly identified by an increase in deformation. In the case of no heating effects, a minimal model for drop deformation in an optical stretcher and a more specific model for vesicle deformation that takes explicitly into account the angular dependence of the optical stress are presented to account for the experimental results. Elastic constants are extracted from the fitting procedures, which agree with literature data. This study demonstrates the utility of optical stretching, which is easily combined with microfluidic delivery, for the future serial, high-throughput study of the mechanical and thermodynamic properties of phospholipid vesicles.

41 citations

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TL;DR: In this paper, a thermodynamically consistent minimal lattice model that includes the chemical reaction providing the propulsion and ordinary translational noise was proposed to identify the physical entropy production of an active particle in an external potential.
Abstract: Entropy production of an active particle in an external potential is identified through a thermodynamically consistent minimal lattice model that includes the chemical reaction providing the propulsion and ordinary translational noise. In the continuum limit, a unique expression follows, comprising a direct contribution from the active process and an indirect contribution from ordinary diffusive motion. From the corresponding Langevin equation, this physical entropy production cannot be inferred through the conventional, yet here ambiguous, comparison of forward and time-reversed trajectories. Generalizations to several interacting active particles and passive particles in a bath of active ones are presented explicitly, further ones are briefly indicated.

40 citations

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TL;DR: Two different theoretical variants of a generalized fluctuation-dissipation theorem are validated and it is demonstrated that the choice of observables crucially affects the accuracy of determining the nonequ equilibrium response from steady state nonequilibrium fluctuations.
Abstract: We study the fluctuation-dissipation theorem for a Brownian particle driven into a nonequilibrium steady state experimentally. We validate two different theoretical variants of a generalized fluctuation-dissipation theorem. Furthermore, we demonstrate that the choice of observables crucially affects the accuracy of determining the nonequilibrium response from steady state nonequilibrium fluctuations.

39 citations


Cited by
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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.

5,180 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.

3,647 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

3,424 citations