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

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

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

Static and dynamic heterogeneities in a model for irreversible gelation

We study the structure and the dynamics in the formation of irreversible gels by means of molecular dynamics simulation of a model system where the gelation transition is due to the random percolation of permanent bonds between neighboring particles. We analyze the heterogeneities of the dynamics in terms of the fluctuations of the intermediate scattering functions: In the sol phase close to the percolation threshold, we find that this dynamical susceptibility increases with the time until it reaches a plateau. At the gelation threshold this plateau scales as a function of the wave vector $k$ as $k^{\eta -2}$, with $\eta$ being related to the decay of the percolation pair connectedness function. At the lowest wave vector, approaching the gelation threshold it diverges with the same exponent $\gamma$ as the mean cluster size. These findings suggest an alternative way of measuring critical exponents in a system undergoing chemical gelation.Comment: 4 pages, 4 figure

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

Hamiltonian dynamics of homopolymer chain models

The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of observables numerically computed along dynamical trajectories are found to reproduce results given by the statistical mechanics of homopolymer models. The dynamical treatment, however, indicates a nontrivial transition between regimes of slow and fast phase space mixing. Such a transition is inaccessible to a statistical mechanical treatment and reflects a bimodality in the relaxation of time averages to corresponding ensemble averages. It is also found that a change in the energy dependence of the largest Lyapunov exponent indicates the theta-transition between filamentary and globular polymer configurations, clearly detecting the transition even for a finite number of particles.Comment: 11 pages, 8 figures, accepted for publication in Physical Review

The scaling attractor and ultimate dynamics for Smoluchowski's coagulation equations

We describe a basic framework for studying dynamic scaling that has roots in dynamical systems and probability theory. Within this framework, we study Smoluchowski's coagulation equation for the three simplest rate kernels $K(x,y)=2$, $x+y$ and $xy$. In another work, we classified all self-similar solutions and all universality classes (domains of attraction) for scaling limits under weak convergence (Comm. Pure Appl. Math 57 (2004)1197-1232). Here we add to this a complete description of the set of all limit points of solutions modulo scaling (the scaling attractor) and the dynamics on this limit set (the ultimate dynamics). The main tool is Bertoin's L\'{e}vy-Khintchine representation formula for eternal solutions of Smoluchowski's equation (Adv. Appl. Prob. 12 (2002) 547--64). This representation linearizes the dynamics on the scaling attractor, revealing these dynamics to be conjugate to a continuous dilation, and chaotic in a classical sense. Furthermore, our study of scaling limits explains how Smoluchowski dynamics ``compactifies'' in a natural way that accounts for clusters of zero and infinite size (dust and gel)

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