Universität Stuttgart
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Item Open Access Adhesion of vesicles and membranes(1991) Lipowsky, Reinhard; Seifert, UdoIn the presence of an attractive surface, a vesicle can undergo shape transformations between two different free states, between a free and a bound state, and between two different bound states. Adhesion can also lead to topological changes such as vesicle rupture and vesicle fusion. The interaction between the vesicle membrane and the surface is renormalized by thermally excited shape fluctuations. This renormalization leads to unbinding phenomena both for fluid and for polymerized (or solid-like) membranes.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 Conformal degeneracy and conformal diffusion of vesicles(1993) Jülicher, Frank; Seifert, Udo; Lipowsky, ReinhardThe shape of vesicles with genus g=2, i.e., with two holes or two handles, is studied in the framework of curvature models. These vesicles exhibit a new phase which also persists for higher genus g>2. In this phase, the ground state of the vesicle is conformally degenerate even when the volume, the area, and the total mean curvature of the vesicle are kept constant. It is predicted that such vesicles undergo a new type of diffusive motion, termed conformal diffusion, which should be observable in experiments as pronounced shape fluctuations.Item Open Access Dual network model for red blood cell membranes(1992) Boal, David H.; Seifert, Udo; Zilker, AndreasA two-component network is studied by Monte Carlo simulation to model the lipid/spectrin membrane of red blood cells. The model predicts that the shear modulus decreases rapidly with the maximum length of the model spectrin and should be in the 10-7 J/m2 range for human red blood cells. A simplified model for the isolated spectrin network shows a negative Lamé coefficient λ. Transverse fluctuations of the dual membrane are found to be fluidlike over the range of wavelengths investigated.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 Budding transitions of fluid-bilayer vesicles: the effect of area-difference elasticity(1994) Miao, Ling; Seifert, Udo; Wortis, Michael; Döbereiner, Hans-GüntherBudding and vesiculation are prominent shape transformations of fluid lipid-bilayer vesicles. We discuss these transitions within the context of a curvature model which contains two types of bending energy. In addition to the usual local curvature elasticity κ, we include the effect of a relative areal stretching of the two monolayers. This area-difference elasticity leads to an effective nonlocal curvature energy characterized by another parameter κ¯. We argue that the two contributions to the curvature energy are typically comparable in magnitude. The model interpolates smoothly between the spontaneous-curvature model (κ¯=0) and the bilayer-couple model (κ¯→∞), discussed previously in the literature. Conceptually, this model is not new; however, neither its consequences nor its relation to experiment has previously been explored in detail. In particular, budding is discontinuous (first order) for small κ¯ but changes via a tricritical point to continuous (second order) for large κ¯. The order of the budding transition depends on both the ratio κ¯/κ (which is a material parameter) and the initial area difference between the inner and outer monolayers (which can be modified by appropriate treatment of the vesicle). Estimates suggest that, under typical laboratory conditions, the budding process should be discontinuous, in apparent disagreement with some recent experiments. Possible reasons for this discrepancy are discussed. We propose, in particular, that hysteretic effects are important and that the observed behavior may reflect a spinodal instability.Item Open Access Efficiencies of a molecular motor : a generic hybrid model applied to the F1-ATPase(2012) Zimmermann, Eva; Seifert, UdoIn a single-molecule assay, the motion of a molecular motor is often inferred by measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic setup taking into account explicitly the elastic coupling between the probe and the motor. The combined dynamics consists of discrete steps of the motor and the continuous Brownian motion of the probe. Motivated by recent experiments on the F1-ATPase, we investigated three types of efficiencies both in simulations and in a Gaussian approximation. Overall, we obtained good quantitative agreement with the experimental data. In particular, we clarify the conditions under which one of these efficiencies becomes larger than 1.Item Open Access Vesicles of toroidal topology(1991) Seifert, UdoWe consider fluid vesicles of toroidal topology. Minimization of the curvature energy at fixed volume and area leads to three different branches of axisymmetric shapes. By using conformal transformations, we identify a large region of nonaxisymmetric shapes in the phase diagram. For vanishing spontaneous curvature, the ground state is twofold degenerate in this region and corresponds to zero pressure difference across the membrane. The relation of these results to the recent observation of toroidal shapes for partially polymerized vesicles is discussed.Item Open Access Non-Markovian description of the Hedvall effect(1987) Seifert, Udo; Dietrich, SiegfriedActivated processes at surfaces - like desorption or oxidation - exhibit thermal anomalies at phase transitions or the underlying substrate. Inter alia, such singularities in the case of a continuous transition are caused by the critical slowing down in the substrate, which leads to pronounced memory effects in the viscosity coefficient. Therefore, we apply a non-Markovian analog of Kramers' classical rate theory. As a result, the anomalies can be expressed in terms of critical exponents associated with the critical surface behaviour.