Equilibrium properties of charged microgels: a Poisson-Boltzmann-Flory approach

The equilibrium properties of ionic microgels are investigated using a combination of the Poisson-Boltzmann and Flory theories. Swelling behavior, density profiles, and effective charges are all calculated in a self-consistent way. Special attention is given to the effects of salinity on these quantities. It is found that the equilibrium microgel size is strongly influenced by the amount of added salt. Increasing the salt concentration leads to a considerable reduction of the microgel volume, which therefore releases its internal material -- solvent molecules and dissociated ions -- into the solution. Finally, the question of charge renormalization of ionic microgels in the context of the cell model is briefly addressed

Simplified Onsager theory for isotropic-nematic phase equilibria of length polydisperse hard rods

Polydispersity is believed to have important effects on the formation of liquid crystal phases in suspensions of rod-like particles. To understand such effects, we analyse the phase behaviour of thin hard rods with length polydispersity. Our treatment is based on a simplified Onsager theory, obtained by truncating the series expansion of the angular dependence of the excluded volume. We describe the model and give the full phase equilibrium equations; these are then solved numerically using the moment free energy method which reduces the problem from one with an infinite number of conserved densities to one with a finite number of effective densities that are moments of the full density distribution. The method yields exactly the onset of nematic ordering. Beyond this, results are approximate but we show that they can be made essentially arbitrarily precise by adding adaptively chosen extra moments, while still avoiding the numerical complications of a direct solution of the full phase equilibrium conditions. We investigate in detail the phase behaviour of systems with three different length distributions: a (unimodal) Schulz distribution, a bidisperse distribution and a bimodal mixture of two Schulz distributions which interpolates between these two cases. A three-phase isotropic-nematic-nematic coexistence region is shown to exist for the bimodal and bidisperse length distributions if the ratio of long and short rod lengths is sufficiently large, but not for the unimodal one. We systematically explore the topology of the phase diagram as a function of the width of the length distribution and of the rod length ratio in the bidisperse and bimodal cases.Comment: 18 pages, 16 figure

Topological Solitons and Folded Proteins

We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by assembling the solitons together, one after another. We present a simple theoretical model that realizes our proposal and apply it to a number of biologically active proteins including 1VII, 2RB8, 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to construct solitons that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 0.7 Angstrom or less for the central alpha-carbons, i.e. within the limits of current experimental accuracy.Comment: 4 pages, 4 figure

A graph theoretical analysis of the energy landscape of model polymers

In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have non trivial effects on such networks and must be taken into account. We do this by means of a recently proposed renormalization procedure. This method is applied to analyze the topology of the network of metastable states for different polypeptidic sequences in a minimalistic polymer model. A smaller spectral dimension emerges as a hallmark of stability of the global energy minimum and highlights a non-obvious link between dynamic and thermodynamic properties.Comment: 15 pages, 15 figure

The Branched Polymer Growth Model Revisited

The Branched Polymer Growth Model (BPGM) has been employed to study the kinetic growth of ramified polymers in the presence of impurities. In this article, the BPGM is revisited on the square lattice and a subtle modification in its dynamics is proposed in order to adapt it to a scenario closer to reality and experimentation. This new version of the model is denominated the Adapted Branched Polymer Growth Model (ABPGM). It is shown that the ABPGM preserves the functionalities of the monomers and so recovers the branching probability b as an input parameter which effectively controls the relative incidence of bifurcations. The critical locus separating infinite from finite growth regimes of the ABPGM is obtained in the (b,c) space (where c is the impurity concentration). Unlike the original model, the phase diagram of the ABPGM exhibits a peculiar reentrance.Comment: 8 pages, 10 figures. To be published in PHYSICA

Long Range Bond-Bond Correlations in Dense Polymer Solutions

The scaling of the bond-bond correlation function $C(s)$ along linear polymer chains is investigated with respect to the curvilinear distance, $s$, along the flexible chain and the monomer density, $\rho$, via Monte Carlo and molecular dynamics simulations. % Surprisingly, the correlations in dense three dimensional solutions are found to decay with a power law $C(s) \sim s^{-\omega}$ with $\omega=3/2$ and the exponential behavior commonly assumed is clearly ruled out for long chains. % In semidilute solutions, the density dependent scaling of $C(s) \approx g^{-\omega_0} (s/g)^{-\omega}$ with $\omega_0=2-2\nu=0.824$ ($\nu=0.588$ being Flory's exponent) is set by the number of monomers $g(\rho)$ contained in an excluded volume blob of size $\xi$. % Our computational findings compare well with simple scaling arguments and perturbation calculation. The power-law behavior is due to self-interactions of chains on distances $s \gg g$ caused by the connectivity of chains and the incompressibility of the melt. %Comment: 4 pages, 4 figure

Colloid-Induced Polymer Compression

We consider a model mixture of hard colloidal spheres and non-adsorbing polymer chains in a theta solvent. The polymer component is modelled as a polydisperse mixture of effective spheres, mutually noninteracting but excluded from the colloids, with radii that are free to adjust to allow for colloid-induced compression. We investigate the bulk fluid demixing behaviour of this model system using a geometry-based density-functional theory that includes the polymer size polydispersity and configurational free energy, obtained from the exact radius-of-gyration distribution for an ideal (random-walk) chain. Free energies are computed by minimizing the free energy functional with respect to the polymer size distribution. With increasing colloid concentration and polymer-to-colloid size ratio, colloidal confinement is found to increasingly compress the polymers. Correspondingly, the demixing fluid binodal shifts, compared to the incompressible-polymer binodal, to higher polymer densities on the colloid-rich branch, stabilizing the mixed phase.Comment: 14 pages, 4 figure

Effective interactions between star polymers and colloidal particles

Using monomer-resolved Molecular Dynamics simulations and theoretical arguments based on the radial dependence of the osmotic pressure in the interior of a star, we systematically investigate the effective interactions between hard, colloidal particles and star polymers in a good solvent. The relevant parameters are the size ratio q between the stars and the colloids, as well as the number of polymeric arms f (functionality) attached to the common center of the star. By covering a wide range of q's ranging from zero (star against a flat wall) up to about 0.75, we establish analytical forms for the star-colloid interaction which are in excellent agreement with simulation results. A modified expression for the star-star interaction for low functionalities, f < 10 is also introduced.Comment: 37 pages, 14 figures, preprint-versio

Percolation and jamming in random sequential adsorption of linear segments on square lattice

We present the results of study of random sequential adsorption of linear segments (needles) on sites of a square lattice. We show that the percolation threshold is a nonmonotonic function of the length of the adsorbed needle, showing a minimum for a certain length of the needles, while the jamming threshold decreases to a constant with a power law. The ratio of the two thresholds is also nonmonotonic and it remains constant only in a restricted range of the needles length. We determine the values of the correlation length exponent for percolation, jamming and their ratio