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

Metastable tight knots in a worm-like polymer

Based on an estimate of the knot entropy of a worm-like chain we predict that the interplay of bending energy and confinement entropy will result in a compact metastable configuration of the knot that will diffuse, without spreading, along the contour of the semi-flexible polymer until it reaches one of the chain ends. Our estimate of the size of the knot as a function of its topological invariant (ideal aspect ratio) agrees with recent experimental results of knotted dsDNA. Further experimental tests of our ideas are proposed.Comment: 4 pages, 3 figure

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

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

Collapsed 2-Dimensional Polymers on a Cylinder

Single partially confined collapsed polymers are studied in two dimensions. They are described by self-avoiding random walks with nearest-neighbour attractions below the $\Theta$-point, on the surface of an infinitely long cylinder. For the simulations we employ the pruned-enriched-Rosenbluth method (PERM). The same model had previously been studied for free polymers (infinite lattice, no boundaries) and for polymers on finite lattices with periodic boundary conditions. We verify the previous estimates of bulk densities, bulk free energies, and surface tensions. We find that the free energy of a polymer with fixed length $N$ has, for $N\to \infty$, a minimum at a finite cylinder radius $R^*$ which diverges as $T\to T_\theta$. Furthermore, the surface tension vanishes roughly as $(T_\theta-T)^\alpha$ for $T\to T_\theta$ with $\alpha\approx 1.7$. The density in the interior of a globule scales as $(T_\theta-T)^\beta$ with $\beta \approx 0.32$.Comment: 4 pages, 8 figure

Error-proof programmable self-assembly of DNA-nanoparticle clusters

We study theoretically a new generic scheme of programmable self-assembly of nanoparticles into clusters of desired geometry. The problem is motivated by the feasibility of highly selective DNA-mediated interactions between colloidal particles. By analyzing both a simple generic model and a more realistic description of a DNA-colloidal system, we demonstrate that it is possible to suppress the glassy behavior of the system, and to make the self-assembly nearly error-proof. This regime requires a combination of stretchable interparticle linkers (e.g. sufficiently long DNA), and a soft repulsive potential. The jamming phase diagram and the error probability are computed for several types of clusters. The prospects for the experimental implementation of our scheme are also discussed. PACS numbers: 81.16.Dn, 87.14.Gg, 36.40.EiComment: 6 pages, 4 figures, v2: substantially revised version, added journal re

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

Localization in simple multiparticle catalytic absorption model

We consider the phase transition in the system of n simultaneously developing random walks on the halfline x>=0. All walks are independent on each others in all points except the origin x=0, where the point well is located. The well depth depends on the number of particles simultaneously staying at x=0. We consider the limit n>>1 and show that if the depth growth faster than 3/2 n ln(n) with n, then all random walks become localized simultaneously at the origin. In conclusion we discuss the connection of that problem with the phase transition in the copolymer chain with quenched random sequence of monomers considered in the frameworks of replica approach.Comment: 17 pages in LaTeX, 5 PostScript figures; submitted to J.Phys.(A): Math. Ge

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

On the Limits of Analogy Between Self-Avoidance and Topology-Driven Swelling of Polymer Loops

The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops is described and shown to agree with simulation data. Contrast between this expression and the well known expression for excluded volume polymers leads to a graphical mapping of excluded volume to trivial knots, which may be useful for understanding where the analogy between the two physical forms is valid. The work also includes description of a new method for the computational generation of polymer loops via conditional probability. Although computationally intensive, this method generates loops without statistical bias, and thus is preferable to other loop generation routines in the region $N<N_0$.Comment: 10 pages, 5 figures, supplementary tex file and datafil