arXiv subjects

Erwin Frey

Publications and source records attributed to Erwin Frey.

At least 181 records · Page 10Linked to original sources

arXiv2006

Bulk-driven non-equilibrium phase transitions in a mesoscopic ring

We study a periodic one-dimensional exclusion process composed of a driven and a diffusive part. In a mesoscopic limit where both dynamics compete we identify bulk-driven phase transitions. We employ mean-field theory complemented by Monte-Carlo simulations to characterize the emerging non-equilibrium steady states. Monte-Carlo simulations reveal interesting correlation effects that we explain phenomenologically.

cond-mat.stat-mech↗

arXiv2006

Floppy modes and non-affine deformations in random fiber networks

We study the elasticity of random fiber networks. Starting from a microscopic picture of the non-affine deformation fields we calculate the macroscopic elastic moduli both in a scaling theory and a self-consistent effective medium theory. By relating non-affinity to the low-energy excitations of the network (``floppy-modes'') we achieve a detailed characterization of the non-affine deformations present in fibrous networks.

cond-mat.soft↗

arXiv2006

Spin models for orientational ordering of colloidal molecular crystals

Two-dimensional colloidal suspensions exposed to periodic external fields exhibit a variety of molecular crystalline phases. There two or more colloids assemble at lattice sites of potential minima to build new structural entities, referred to as molecules. Using the strength of the potential and the filling fraction as control parameter, phase transition to unconventional orientationally ordered states can be induced. We introduce an approach that focuses at the discrete set of orientational states relevant for the phase ordering. The orientationally ordered states are mapped to classical spin systems. We construct effective hamiltonians for dimeric and trimeric molecules on triangular lattices suitable for a statistical mechanics discussion. A mean-field analysis produces a rich phase behavior which is substantiated by Monte Carlo simulations.

cond-mat.soft↗

arXiv2006

Localization Transition of the Three-Dimensional Lorentz Model and Continuum Percolation

The localization transition and the critical properties of the Lorentz model in three dimensions are investigated by computer simulations. We give a coherent and quantitative explanation of the dynamics in terms of continuum percolation theory, an excellent matching of both the critical density and exponents is obtained. Upon exploiting a dynamic scaling Ansatz employing two divergent length scales we find data collapse for the mean-square displacements and identify the leading-order corrections to scaling. The non-Gaussian parameter is predicted to diverge at the transition.

cond-mat.soft↗

arXiv2006

Entropic forces generated by grafted semiflexible polymers

The entropic force exerted by the Brownian fluctuations of a grafted semiflexible polymer upon a rigid smooth wall are calculated both analytically and by Monte Carlo simulations. Such forces are thought to play an important role for several cellular phenomena, in particular, the physics of actin-polymerization-driven cell motility and movement of bacteria like Listeria. In the stiff limit, where the persistence length of the polymer is larger than its contour length, we find that the entropic force shows scaling behavior. We identify the characteristic length scales and the explicit form of the scaling functions. In certain asymptotic regimes we give simple analytical expressions which describe the full results to a very high numerical accuracy. Depending on the constraints imposed on the transverse fluctuations of the filament there are characteristic differences in the functional form of the entropic forces; in a two-dimensional geometry the entropic force exhibits a marked peak.

cond-mat.soft↗

arXiv2005

Renewal processes and fluctuation analysis of molecular motor stepping

We model the dynamics of a processive or rotary molecular motor using a renewal processes, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation functions of the renewal process, which have applications to bead-assay experiments performed both with processive molecular motors, such as myosin V and kinesin, and rotary motors, such as F1-ATPase.

cond-mat.stat-mech↗

arXiv2005

Oscillations in molecular motor assemblies

Autonomous oscillations in biological systems may have a biochemical origin or result from an interplay between force-generating and visco-elastic elements. In molecular motor assemblies the force-generating elements are molecular engines and the visco-elastic elements are stiff cytoskeletal polymers. The physical mechanism leading to oscillations depends on the particular architecture of the assembly. Existing models can be grouped into two distinct categories: systems with a delayed force activation and anomalous force-velocity relations. We discuss these systems within phase plane analysis known from the theory of dynamic systems and by adopting methods from control theory, the Nyquist stability criterion.

physics.bio-ph↗

arXiv2005

Elastic properties of grafted microtubules

We use single-particle tracking to study the elastic properties of single microtubules grafted to a substrate. Thermal fluctuations of the free microtubule's end are recorded, in order to measure position distribution functions from which we calculate the persistence length of microtubules with contour lengths between 2.6 and 48 micrometers. We find the persistence length to vary by more than a factor of 20 over the total range of contour lengths. Our results support the hypothesis that shearing between protofilaments contributes significantly to the mechanics of microtubules.

q-bio.BM↗

arXiv2005

Stiff Polymers, Foams and Fiber Networks

We study the elasticity of fibrous materials composed of generalized stiff polymers. It is shown that in contrast to cellular foam-like structures affine strain fields are generically unstable. Instead, a subtle interplay between the architecture of the network and the elastic properties of its building blocks leads to intriguing mechanical properties with intermediate asymptotic scaling regimes. We present exhaustive numerical studies based on a finite element method complemented by scaling arguments.

cond-mat.soft↗

arXiv2005

Propagation and Relaxation of Tension in Stiff Polymers

We present a unified theory for the longitudinal dynamic response of a stiff polymer in solution to various external perturbations (mechanical excitations, hydrodynamic flows, electrical fields, temperature quenches ...) that can be represented as sudden changes of ambient/boundary conditions. The theory relies on a comprehensive analysis of the non--equilibrium propagation and relaxation of backbone stresses in a wormlike chain. We recover and substantially extend previous results based on heuristic arguments. Intriguing new experimental implications are pointed out.

cond-mat.soft↗

arXiv2005

Brownian motion: a paradigm of soft matter and biological physics

This is a pedagogical introduction to Brownian motion on the occasion of the 100th anniversary of Einstein's 1905 paper on the subject. After briefly reviewing Einstein's work in its contemporary context, we pursue some lines of further developments and applications in soft condensed matter and biology. Over the last century Brownian motion became promoted from an odd curiosity of marginal scientific interest to a guiding theme pervading all of the modern (live) sciences.

cond-mat.soft↗

arXiv2004

Linear response of a grafted semiflexible polymer to a uniform force field

We use the worm-like chain model to analytically calculate the linear response of a grafted semiflexible polymer to a uniform force field. The result is a function of the bending stiffness, the temperature, the total contour length, and the orientation of the field with respect to that of the grafted end. We also study the linear response of a worm-like chain with a periodic alternating sequence of positive and negative charges. This can be considered as a model for a polyampholyte with intrinsic bending siffness and negligible intramolecular interactions. We show how the finite intrinsic persistence length affects the linear response to the external field.

cond-mat.soft↗

arXiv2004

Overdamped Stress Relaxation in Buckled Rods

We present a comprehensive theoretical analysis of the stress relaxation in a multiply but weakly buckled incompressible rod in a viscous solvent. In the bulk two interesting regimes of generic self--similar intermediate asymptotics are distinguished, which give rise to two classes of approximate and exact power--law solutions, respectively. For the case of open boundary conditions the corresponding non--trivial boundary--layer scenarios are derived by a multiple--scale perturbation (``adiabatic'') method. Our results compare well with -- and provide the theoretical explanation for -- previous results from numerical simulations, and they suggest new directions for further fruitful numerical and experimental investigations.

cond-mat.soft↗

arXiv2003

Transverse fluctuations of grafted polymers

We study the statistical mechanics of grafted polymers of arbitrary stiffness in a two-dimensional embedding space with Monte Carlo simulations. The probability distribution function of the free end is found to be highly anisotropic and non-Gaussian for typical semiflexible polymers. The reduced distribution in the transverse direction, a Gaussian in the stiff and flexible limits, shows a double peak structure at intermediate stiffnesses. We also explore the response to a transverse force applied at the polymer free end. We identify F-Actin as an ideal benchmark for the effects discussed.

physics.bio-ph↗

arXiv2003

Internal Motility in Stiffening Actin-Myosin Networks

We present a study on filamentous actin solutions containing heavy meromyosin subfragments of myosin II motor molecules. We focus on the viscoelastic phase behavior and internal dynamics of such networks during ATP depletion. Upon simultaneously using micro-rheology and fluorescence microscopy as complementary experimental tools, we find a sol-gel transition accompanied by a sudden onset of directed filament motion. We interpret the sol-gel transition in terms of myosin II enzymology, and suggest a "zipping" mechanism to explain the filament motion in the vicinity of the sol-gel transition.

physics.bio-ph↗

arXiv2003

Elasticity of Stiff Polymer Networks

We study the elasticity of a two-dimensional random network of rigid rods (``Mikado model''). The essential features incorporated into the model are the anisotropic elasticity of the rods and the random geometry of the network. We show that there are three distinct scaling regimes, characterized by two distinct length scales on the elastic backbone. In addition to a critical rigidiy percolation region and a homogeneously elastic regime we find a novel intermediate scaling regime, where elasticity is dominated by bending deformations.

cond-mat.soft↗

arXiv2002

Depinning of semiflexible polymers in (1+1) dimensions

We present a theoretical analysis of a simple model of the depinning of an anchored semiflexible polymer from a fixed planar substrate in (1+1) dimensions. We consider a polymer with a discrete sequence of pinning sites along its contour. Using the scaling properties of the conformational distribution function in the stiff limit and applying the necklace model of phase transitions in quasi-one-dimensional systems, we obtain a melting criterion in terms of the persistence length, the spacing between pinning sites, a microscopic effective length which characterizes a bond, and the bond energy. The limitations of this and other similar approaches are also discussed. In the case of force-induced unbinding, it is shown that the bending rigidity favors the unbinding through a ``lever-arm effect''.

cond-mat.soft↗

arXiv2002

Anomalous relaxation kinetics of biological lattice-ligand binding models

We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric constraints, size of ligands, binding rates and interaction between neighboring proteins on the binding dynamics and binding stoichiometry. Starting from an empty lattice the binding dynamics goes, quite generally, through several stages. The first stage represents fast initial binding closely resembling the physics of random sequential adsorption processes. Typically this initial process leaves the system in a metastable locked state with many small gaps between blocks of bound molecules. In a second stage the gaps annihilate slowly as the ligands detach and reattach. This results in an algebraic decay of the gap concentration and interesting scaling behavior. Upon identifying the gaps with particles we show that the dynamics in this regime can be explained by mapping it onto various reaction-diffusion models. The final approach to equilibrium shows some interesting dynamic scaling properties. We also discuss the effect of cooperativity on the equilibrium stoichiometry, and their consequences for the interpretation of biochemical and image reconstruction results.

cond-mat.soft↗