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.

Entropy production for mechanically or chemically driven biomolecules

Abstract: Entropy production along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium. For a molecule manipulated mechanically by an AFM or an optical tweezer, entropy production (or annihilation) occurs in the molecular conformation proper or in the surrounding medium. Within a Langevin dynamics, a unique identification of these two contributions is possible. The total entropy change obeys an integral fluctuation theorem and a class of further exact relations, which we prove for arbitrarily coupled slow degrees of freedom including hydrodynamic interactions. These theoretical results can therefore also be applied to driven colloidal systems. For transitions between different internal conformations of a biomolecule involving unbalanced chemical reactions, we provide a thermodynamically consistent formulation and identify again the two sources of entropy production, which obey similar exact relations. We clarify the particular role degenerate states have in such a description.

Propagator for a driven Brownian particle in step potentials

Abstract: Although driven Brownian particles are ubiquitous in stochastic dynamics and often serve as paradigmatic model systems for many aspects of stochastic thermodynamics, fully analytically solvable models are few and far between. In this paper, we introduce an iterative calculation scheme, similar to the method of images in electrostatics, that enables one to obtain the propagator if the potential consists of a finite number of steps. For the special case of a single potential step, this method converges after one iteration, thus providing an expression for the propagator in closed form. In all other cases, the iteration results in an approximation that holds for times smaller than some characteristic timescale that depends on the number of iterations performed. This method can also be applied to a related class of systems like Brownian ratchets, which do not formally contain step potentials in their definition, but impose the same kind of boundary conditions that are caused by potential steps.

Front Propagation in the Pearling Instability of Tubular Vesicles

Abstract: Recently Bar-Ziv and Moses discovered a dynamical shape transformation induced in cylindrical lipid bilayer vesicles by the action of laser tweezers. We develop a hydrodynamic theory of fluid bilayers in interaction with the surrounding water and argue that the effect of the laser is to induce a sudden tension in the membrane. We refine our previous analysis to account for the fact that the shape transformation is not uniform but propagates outward from the laser trap. Applying the marginal stability criterion to this situation gives us an improved prediction for the selected initial wavelength and a new prediction for the propagation velocity, both in rough agreement with the experimental values. For example, a tubule of initial radius 0.7\micron\ has a predicted initial sinusoidal perturbation in its diameter with wavelength 5.5\micron, as observed. The perturbation propagates as a front with the qualitatively correct front velocity a bit less than 100\micron/sec. In particular we show why this velocity is initially constant, as observed, and so much smaller than the natural scale set by the tension. We also predict that the front velocity should increase linearly with laser power. Finally we introduce an approximate hydrodynamic model applicable to the fully nonlinear regime. This model exhibits propagating fronts as well as fully-developed ``pearled" vesicles similar to those seen in the experiments.

Interlinked GTPase cascades provide a motif for both robust switches and oscillators

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.

Fluid bilayer vesicles Statistical physics of soft two-dimensional surfaces

Abstract: The combination of length-xales of several microns, time scales for dynamic fluctuations accessible to video frequency, and energy scales of a few kbT all contribute to make vesicles a unique model system to study the statistical physics of soft surfaces in real space.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

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。

Reaction-rate theory: fifty years after Kramers

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.

Stochastic Processes in Physics and Chemistry

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.

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

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