Adsorption of a random heteropolymer at a potential well revisited: location of transition point and design of sequences

The adsorption of an ideal heteropolymer loop at a potential point well is investigated within the frameworks of a standard random matrix theory. On the basis of semi-analytical/semi-numerical approach the histogram of transition points for the ensemble of quenched heteropolymer structures with bimodal symmetric distribution of types of chain's links is constructed. It is shown that the sequences having the transition points in the tail of the histogram display the correlations between nearest-neighbor monomers.Comment: 11 pages (revtex), 3 figure

How long does it take to pull an ideal polymer into a small hole?

We present scaling estimates for characteristic times $\tau_{\rm lin}$ and $\tau_{\rm br}$ of pulling ideal linear and randomly branched polymers of $N$ monomers into a small hole by a force $f$. We show that the absorbtion process develops as sequential straightening of folds of the initial polymer configuration. By estimating the typical size of the fold involved into the motion, we arrive at the following predictions: $\tau_{\rm lin}(N) \sim N^{3/2}/f$ and $\tau_{\rm br}(N) \sim N^{5/4}/f$, and we also confirm them by the molecular dynamics experiment.Comment: 4 pages, 3 figure

Single-file dynamics with different diffusion constants

We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore interacting particles (the particles cannot pass each other) which are diffusing in a one-dimensional system where the particles have different diffusion constants. For the two particle case an exact result for the conditional probability density function (PDF) is obtained for arbitrary initial particle positions and all times. The two-particle PDF is used to obtain the tagged particle PDF. For the general N-particle case (N large) we perform stochastic simulations using our new computationally efficient stochastic simulation technique based on the Gillespie algorithm. We find that the mean square displacement for a tagged particle scales as the square root of time (as for identical particles) for long times, with a prefactor which depends on the diffusion constants for the particles; these results are in excellent agreement with very recent analytic predictions in the mathematics literature.Comment: 9 pages, 5 figures. Journal of Chemical Physics (in press

A coil-globule transition of a semiflexible polymer driven by the addition of spherical particles

The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of magnitude larger than the diameter of the polymer. The spherical particles induce a quite long ranged depletion attraction between the segments of the polymer and this induces a continuous coil-globule transition in the polymer. This behaviour gives an indication of the condensing effect of macromolecular crowding on DNA.Comment: 12 pages, 4 figure

Crowding effect on helix-coil transition: beyond entropic stabilization

We report circular dichroism measurements on the helix-coil transition of poly(L-glutamic acid) in solution with polyethylene glycol (PEG) as a crowding agent. Using small angle neutron scattering, PEG solutions have been characterized and found to be well described by the picture of a transient network of mesh size $\xi$, usual for semi-diluted chains in good solvent. We show that the increase of PEG concentration stabilizes the helices and increases the transition temperature. But more unexpectedly we also notice that the increase of crowding agent concentration reduces the mean helix extent at the transition, or in other words reduces its cooperative feature. This result cannot be accounted for by an entropic stabilization mechanism. Comparing the mean length of helices at the transition and the mesh size of the PEG network, our results strongly suggest two regimes: helices shorter or longer than the mesh size

Rheology of Ring Polymer Melts: From Linear Contaminants to Ring/Linear Blends

Ring polymers remain a major challenge to our current understanding of polymer dynamics. Experimental results are difficult to interpret because of the uncertainty in the purity and dispersity of the sample. Using both equilibrium and non-equilibrium molecular dynamics simulations we have systematically investigated the structure, dynamics and rheology of perfectly controlled ring/linear polymer blends with chains of such length and flexibility that the number of entanglements is up to about 14 per chain, which is comparable to experimental systems examined in the literature. The smallest concentration at which linear contaminants increase the zero-shear viscosity of a ring polymer melt of these chain lengths by 10% is approximately one-fifth of their overlap concentration. When the two architectures are present in equal amounts the viscosity of the blend is approximately twice as large as that of the pure linear melt. At this concentration the diffusion coefficient of the rings is found to decrease dramatically, while the static and dynamic properties of the linear polymers are mostly unaffected. Our results are supported by a primitive path analysis.Comment: 5 pages, 4 figures, accepted by PR

Shear Banding from lattice kinetic models with competing interactions

Soft Glassy Materials, Non Linear Rheology, Lattice Kinetic models, frustrated phase separation} We present numerical simulations based on a Boltzmann kinetic model with competing interactions, aimed at characterizating the rheological properties of soft-glassy materials. The lattice kinetic model is shown to reproduce typical signatures of driven soft-glassy flows in confined geometries, such as Herschel-Bulkley rheology, shear-banding and histeresys. This lends further credit to the present lattice kinetic model as a valuable tool for the theoretical/computational investigation of the rheology of driven soft-glassy materials under confinement.Comment: 8 Pages, 5 Figure

Helical, Angular and Radial Ordering in Narrow Capillaries

To enlighten the nature of the order-disorder and order-order transitions in block copolymer melts confined in narrow capillaries we analyze peculiarities of the conventional Landau weak crystallization theory of systems confined to cylindrical geometry. This phenomenological approach provides a quantitative classification of the cylindrical ordered morphologies by expansion of the order parameter spatial distribution into the eigenfunctions of the Laplace operator. The symmetry of the resulting ordered morphologies is shown to strongly depend both on the boundary conditions (wall preference) and the ratio of the cylinder radius and the wave length of the critical order parameter fluctuations, which determine the bulk ordering of the system under consideration. In particular, occurrence of the helical morphologies is a rather general consequence of the imposed cylindrical symmetry for narrow enough capillaries. We discuss also the ODT and OOT involving some other simplest morphologies. The presented results are relevant also to other ordering systems as charge-density waves appearing under addition of an ionic solute to a solvent in its critical region, weakly charged polyelectrolyte solutions in poor solvent, microemulsions etc.Comment: 6 pages, 3 figure

Entropically driven transition to a liquid-crystalline polymer globule

A self-consistent-field theory (SCFT) in the grand canonical ensemble formulation is used to study transitions in a helix-coil multiblock copolymer globule. The helices are modeled as stiff rods. In addition to the established coil-globule transition we show for the first time that, even without explicit rod-rod alignment interaction, the system undergoes a transition to a nematic liquid-crystalline (LC) globular state. The LC-globule formation is driven by the hydrophobic helical segment attraction and the anisotropy of the globule surface energy. The full phase diagram of the copolymer was calculated. It discriminates between an open chain, amorphous globule and LC-globule. This model provides a relatively simple example of the interplay between secondary and tertiary structures in homopolypeptides. Moreover, it gives a simple explanation for the formation of helix bundles in certain globular proteins.Comment: 5 pages, 5 figures, submitted to Europhys. Let