Gradient and vorticity banding

"Banded structures" of macroscopic dimensions can be induced by simple shear flow in many different types of soft matter systems. Depending on whether these bands extend along the gradient or vorticity direction, the banding transition is referred to as "gradient banding" or "vorticity banding," respectively. The main features of gradient banding can be understood on the basis of a relatively simple constitutive equation. This minimal model for gradient banding will be discussed in some detail, and its predictions are shown to explain many of the experimentally observed features. The minimal model assumes a decrease of the shear stress of the homogeneously sheared system with increasing shear rate within a certain shear-rate interval. The possible microscopic origin of the severe shear-thinning behaviour that is necessary for the resulting nonmonotonic flow curves is discussed for a few particular systems. Deviations between experimental observations and predictions by the minimal model are due to obvious simplifications within the scope of the minimal model. The most serious simplifications are the neglect of concentration dependence of the shear stress (or on other degrees of freedom) and of the elastic contributions to the stress, normal stresses, and the possibility of shear-induced phase transitions. The consequences of coupling of stress and concentration will be analyzed in some detail. In contrast to predictions of the minimal model, when coupling to concentration is important, a flow instability can occur that does not require strong shear thinning. Gradient banding is sometimes also observed in glassy- and gel-like systems, as well as in shear-thickening systems. Possible mechanisms that could be at the origin of gradient-band formation in such systems are discussed. Gradient banding can also occur in strongly entangled polymeric systems. Banding in these systems is discussed on the basis of computer simulations. Vorticity banding is less well understood and less extensively investigated experimentally as compared to gradient banding. Possible scenarios that are at the origin of vorticity banding will be discussed. Among other systems, the observed vorticity-banding transition in rod-like colloids is discussed in some detail. It is argued, on the basis of experimental observations for these colloidal systems, that the vorticity-banding instability for such colloidal suspensions is probably related to an elastic instability, reminiscent of the Weissenberg effect in polymeric systems. This mechanism might explain vorticity banding in discontinuously shear-thickening systems and could be at work in other vorticity-banding systems as well. This overview does not include time-dependent phenomena like oscillations and chaotic behaviour

Free energy calculations of small molecules in dense amorphous polymers. Effect on the initial guess configuration in molecular dynamics studies

The excess free energy of small molecules in the amorphous polymers poly(ethylene) and poly(dimethylsiloxane) was calculated, using the test-particle-insertion method. The method was applied to polymer configurations obtained from molecular dynamics simulations with differently prepared initial guess configurations. It was found that the calculated solubility coefficients strongly depend on the quality of the initial guess configuration. Slow compression of dilute systems, during which process only the repulsive parts of the nonbonded Lennard-Jones potentials are taken into account, yields polymer melts which are better relaxed, and which offer lower solubilities for guest molecules compared with polymer melts generated at the experimental density or prepared by compressing boxes with soft-core nonbonded potentials. For the last two methods initial stresses relax by straining the internal modes (bond angles, torsion angles) of the chain

The attachment of α-synuclein to a fiber:A coarse-grain approach

We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson’s disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet. Flexible linkers between the particles enable sampling of the tertiary structure. This novel model is applied here to study the growth of an amyloid fibril, by calculating the free energy profile of a protein attaching to the end of a fibril. The simulation results suggest that the attaching protein readily becomes trapped in a mis-folded state, thereby inhibiting further growth of the fibril until the protein has readjusted to conform to the fibril structure, in line with experimental findings and previous simulations on small fragments of other proteins

\ud The Generation of Curved Clathrin Coats from Flat Plaques

Flat clathrin lattices or ‘plaques’ are commonly believed to be the precursors to clathrin-coated buds and vesicles. The sequence of steps carrying the flat hexagonal lattice into a highly curved polyhedral cage with exactly 12 pentagons remains elusive, however, and the large numbers of disrupted interclathrin connections in previously proposed conversion pathways make these scenarios rather unlikely. The recent notion that clathrin can make controlled small conformational transitions opens new avenues. Simulations with a self-assembling clathrin model suggest that localized conformational changes in a plaque can create sufficiently strong stresses for a dome-like fragment to break apart. The released fragment, which is strongly curved but still hexagonal, may subsequently grow into a cage by recruiting free triskelia from the cytoplasm, thus building all 12 pentagonal faces without recourse to complex topological changes. The critical assembly concentration in a slightly acidic in vitro solution is used to estimate the binding energy of a cage at 25–40 kBT/clathri