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The classical theory of Brownian dynamics follows from coarse-graining the underlying linearized fluctuating hydrodynamics of the solvent. We extend this procedure to globally non-isothermal conditions, requiring only a local thermal equilibration of the solvent. Starting from the conservation laws, we establish the stochastic equations of motion for the fluid momentum fluctuations in the presence of a suspended Brownian particle. These are then contracted to the non-isothermal generalized Langevin description of the suspended particle alone, for which the coupling to stochastic temperature fluctuations is found to be negligible under typical experimental conditions., Comment: 9 pages

We derive generalized Langevin equations for the translational and rotational motion of a heated Brownian particle from the fluctuating hydrodynamics of its non-isothermal solvent. The temperature gradient around the particle couples to the hydrodynamic modes excited by the particle itself so that the resulting noise spectrum is governed by a frequency-dependent temperature. We show how the effective temperatures at which the article coordinates and (angular) velocities appear to be thermalized emerge from this central quantity., Comment: 11 pages, 4 figures

The Brownian motion of a hot nanoparticle is described by an effective Markov theory based on fluctuating hydrodynamics. Its predictions are scrutinized over a wide temperature range using large-scale molecular dynamics simulations of a hot nanoparticle in a Lennard-Jones fluid. The particle positions and momenta are found to be Boltzmann distributed according to distinct effective temperatures $T_\mathrm{HBM}$ and $T_\mathrm{k}$ . For $T_\mathrm{HBM}$ we derive a formally exact theoretical prediction and establish a generalised Einstein relation that links it to directly measurable quantities.

We determine the statistics of the local tube width in F-actin solutions, beyond the usually reported mean value. Our experimental observations are explained by a segment fluid theory based on the binary collision approximation (BCA). In this systematic generalization of the standard mean-field approach effective polymer segments interact via a potential representing the topological constraints. The analytically predicted universal tube width distribution with a stretched tail is in good agreement with the data., Comment: Final version, 5 pages, 4 figures

The relaxation of initially straight semiflexible polymers has been discussed mainly with respect to the longest relaxation time. The biologically relevant non-equilibrium dynamics on shorter times is comparatively poorly understood, partly because "initially straight" can be realized in manifold ways. Combining Brownian dynamics simulations and systematic theory, we demonstrate how different experimental preparations give rise to specific short-time and universal long-time dynamics. We also discuss boundary effects and the onset of the stretch--coil transition., Comment: 14 pages, 5 figures, 3 tables

We provide a comprehensive overview of the current theoretical understanding of the dynamic structure factor of stiff polymers in semidilute solution based on the wormlike chain (WLC) model. We extend previous work by computing exact numerical coefficients and an expression for the dynamic mean square displacement (MSD) of a free polymer and compare various common approximations for the hydrodynamic interactions, which need to be treated accurately if one wants to extract quantitative estimates for model parameters from experimental data. A recent controversy about the initial slope of the dynamic structure factor is thereby resolved. To account for the interactions of the polymer with a surrounding (sticky) polymer solution, we analyze an extension of the WLC model, the glassy wormlike chain (GWLC), which predicts near power-law and logarithmic long-time tails in the dynamic structure factor., Comment: 14 pages, 5 figures, final version

We introduce a new model for the dynamics of a wormlike chain in an environment that gives rise to a rough free energy landscape, which we baptise the glassy wormlike chain. It is obtained from the common wormlike chain by an exponential stretching of the relaxation spectrum of its long-wavelength eigenmodes, controlled by a single stretching parameter. Predictions for pertinent observables such as the dynamic structure factor and the microrheological susceptibility exhibit the characteristics of soft glassy rheology and compare favourably with experimental data for reconstituted cytoskeletal networks and live cells. We speculate about the possible microscopic origin of the stretching, implications for the nonlinear rheology, and the potential physiological significance of our results., Comment: 12 pages, 8 figures. Minor corrections

We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the propagation speed of the backbone tension which is induced in response to stretching. Here, we employ a newly developed unified theory to systematically substantiate, restrict, and extend these approaches. Introducing the practically relevant scenario of a chain equilibrated under some prestretching force $f_\text{pre}$ that is suddenly exposed to a different external force $f_\text{ext}$ at the ends, we give a concise physical explanation of the underlying relaxation processes by means of an intuitive blob picture. We discuss the corresponding intermediate asymptotics, derive results for experimentally relevant observables, and support our conclusions by numerical solutions of the coarse-grained equations of motion for the tension., Comment: 14 pages, 8 figures; final version as published

We present some recent theory and simulation results addressing the phenomena of colloidal gelation at both high and low volume fractions, in the presence of short-range attractive interactions. We discuss the ability of mode-coupling theory and its adaptations to address situations with strong heterogeneity in density and/or dynamics. We include a discussion of the effect of attractions on the shear-thinning and yield behaviour under flow., Comment: 17 pages, 6 figures

Mode-coupling theory (MCT) predicts arrest of colloids in terms of their volume fraction, and the range and depth of the interparticle attraction. We discuss how effective values of these parameters evolve under cluster aggregation. We argue that weak gelation in colloids can be idealized as a two-stage ergodicity breaking: first at short scales (approximated by the bare MCT) and then at larger scales (governed by MCT applied to clusters). The competition between arrest and phase separation is considered in relation to recent experiments. We predict a long-lived `semi-ergodic' phase of mobile clusters, showing logarithmic relaxation close to the gel line., Comment: 4 pages, 3 figures

Observation of salt-induced aggregation of lysozyme at pH = 4.5, 22$^{\circ}$C by optical microscopy revealed four regimes: bicontinuous texture, `beads', large aggregates, and transient gelation. The interaction of a metastable liquid-liquid binodal and an ergodic to non-ergodic transition boundary inside the equilibrium crystallization region can explain our findings. Lysozyme data at -2$^{\circ}$C, as well as many literature results, are consistent with the relative movement of these boundaries., Comment: 4 pages, 4 figures

Considering the example of interacting Brownian particles we present a linear response derivation of the boundary condition for the corresponding hydrodynamic description (the diffusion equation). This requires us to identify a non-analytic structure in a microscopic relaxation kernel connected to the frequency dependent penetration length familiar for diffusive processes, and leads to a microscopic definition of the position where the hydrodynamic boundary condition has to be applied. Corrections to the hydrodynamic limit are obtained and we derive general amplitudes of spatially and temporally long ranged states in the considered diffusive system., Comment: 15 pages; slightly revised and shortened version; J. Phys.: Condens. Matter in print

We present a model to describe the collective motion of barchan dunes in a field. Our model is able to reproduce the observation that a typical dune stays confined within a stripe. We also obtain some of the pattern structures which ressemble those observed from aerial photos which we do analyse and compare with the specific field of La\^ayounne., Comment: 15 pages, 13 figures

We derive a phenomenological continuum saltation model for aeolian sand transport that can serve as an efficient tool for geomorphological applications. The coupled differential equations for the average density and velocity of sand in the saltation layer reproduce both known equilibrium relations for the sand flux and the time evolution of the sand flux as predicted by microscopic saltation models. The three phenomenological parameters of the model are a reference height for the grain-air interaction, an effective restitution coefficient for the grain-bed interaction, and a multiplication factor characterizing the chain reaction caused by the impacts leading to a typical time or length scale of the saturation transients. We determine the values of these parameters by comparing our model with wind tunnel measurements. Our main interest are out of equilibrium situations where saturation transients are important, for instance at phase boundaries (ground/sand) or under unsteady wind conditions. We point out that saturation transients are indispensable for a proper description of sand flux over structured terrain, by applying the model to the windward side of an isolated dune, thereby resolving recently reported discrepancies between field measurements and theoretical predictions., Comment: 11 pages, 7 figures

We have investigated the viscosity and the plateau modulus of actin solutions with a magnetically driven rotating disc rheometer. For entangled solutions we observed a scaling of the plateau modulus versus concentration with a power of 7/5. The measured terminal relaxation time increases with a power 3/2 as a function of polymer length. We interpret the entanglement transition and the scaling of the plateau modulus in terms of the tube model for semiflexible polymers., Comment: 5 pages, 4 figures, published version

Quasi-elastic light scattering (QELS) is applied to investigate the effect of the tropomyosin/troponin complex (Tm/Tn) on the stiffness of actin filaments. The importance of hydrodynamic screening in semidilute solutions is demonstrated. A new concentration dependent expression for the dynamic structure factor $g(\bm k,t)$ of semiflexible polymers in semidilute solutions is used to analyze the experimental QELS data. A concentration independent value for the bending modulus $\kappa$ is thus obtained. It increases by 50\% as a consequence of Tm/Tn binding in a 7:1:1 molar ratio of actin/Tm/Tn. In addition a new expression for the initial slope of the dynamic structure factor of a semiflexible polymer is used to determine the effective hydrodynamic diameter of the actin filament. Our results confirm the general relevance of the concept of (intrinsic) semiflexibility to polymer dynamics., Comment: 9 pages, RevTeX, 9 figures, all uuencoded gziped