Monte Carlo Results for Projected Self-Avoiding Polygons: A Two-dimensional Model for Knotted Polymers

We introduce a two-dimensional lattice model for the description of knotted polymer rings. A polymer configuration is modeled by a closed polygon drawn on the square diagonal lattice, with possible crossings describing pairs of strands of polymer passing on top of each other. Each polygon configuration can be viewed as the two- dimensional projection of a particular knot. We study numerically the statistics of large polygons with a fixed knot type, using a generalization of the BFACF algorithm for self-avoiding walks. This new algorithm incorporates both the displacement of crossings and the three types of Reidemeister transformations preserving the knot topology. Its ergodicity within a fixed knot type is not proven here rigorously but strong arguments in favor of this ergodicity are given together with a tentative sketch of proof. Assuming this ergodicity, we obtain numerically the following results for the statistics of knotted polygons: In the limit of a low crossing fugacity, we find a localization along the polygon of all the primary factors forming the knot. Increasing the crossing fugacity gives rise to a transition from a self-avoiding walk to a branched polymer behavior.Comment: 36 pages, 30 figures, latex, epsf. to appear in J.Phys.A: Math. Ge

Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes

The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task requires to close the open arcs into a ring, and the resulting topological state may depend on the specific closure scheme that is followed. To understand the impact of this ambiguity in contexts of practical interest, such as knot localization in a ring with non trivial topology, we apply various closure schemes to model ring polymers. The rings have the same length and topological state (a trefoil knot) but have different degree of compactness. The comparison suggests that a novel method, termed the minimally-interfering closure, can be profitably used to characterize the arc entanglement in a robust and computationally-efficient way. This closure method is finally applied to the knot localization problem which is tackled using two different localization schemes based on top-down or bottom-up searches.Comment: 9 pages, 7 figures. Submitted to Progress of Theoretical Physic

Nos\'e-Hoover and Langevin thermostats do not reproduce the nonequilibrium behavior of long-range Hamiltonians

We compare simulations performed using the Nos\'e-Hoover and the Langevin thermostats with the Hamiltonian dynamics of a long-range interacting system in contact with a reservoir. We find that while the statistical mechanics equilibrium properties of the system are recovered by all the different methods, the Nos\'e-Hoover and the Langevin thermostats fail in reproducing the nonequilibrium behavior of such Hamiltonian.Comment: Contribution to the proceeding of the "International Conference on the Frontiers of Nonlinear and Complex Systems" in honor of Prof. Bambi Hu, Hong Kong, May 200

Phase Ordering in Nematic Liquid Crystals

We study the kinetics of the nematic-isotropic transition in a two-dimensional liquid crystal by using a lattice Boltzmann scheme that couples the tensor order parameter and the flow consistently. Unlike in previous studies, we find the time dependences of the correlation function, energy density, and the number of topological defects obey dynamic scaling laws with growth exponents that, within the numerical uncertainties, agree with the value 1/2 expected from simple dimensional analysis. We find that these values are not altered by the hydrodynamic flow. In addition, by examining shallow quenches, we find that the presence of orientational disorder can inhibit amplitude ordering.Comment: 21 pages, 14 eps figures, revte

The entropic cost to tie a knot

We estimate by Monte Carlo simulations the configurational entropy of $N$-steps polygons in the cubic lattice with fixed knot type. By collecting a rich statistics of configurations with very large values of $N$ we are able to analyse the asymptotic behaviour of the partition function of the problem for different knot types. Our results confirm that, in the large $N$ limit, each prime knot is localized in a small region of the polygon, regardless of the possible presence of other knots. Each prime knot component may slide along the unknotted region contributing to the overall configurational entropy with a term proportional to $\ln N$. Furthermore, we discover that the mere existence of a knot requires a well defined entropic cost that scales exponentially with its minimal length. In the case of polygons with composite knots it turns out that the partition function can be simply factorized in terms that depend only on prime components with an additional combinatorial factor that takes into account the statistical property that by interchanging two identical prime knot components in the polygon the corresponding set of overall configuration remains unaltered. Finally, the above results allow to conjecture a sequence of inequalities for the connective constants of polygons whose topology varies within a given family of composite knot types

Interplay between writhe and knotting for swollen and compact polymers

The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo methods to investigate the interplay between writhe and knotting of ring polymers in good and poor solvents. The model that we consider is interacting self-avoiding polygons on the simple cubic lattice. For polygons with fixed knot type we find a writhe distribution whose average depends on the knot type but is insensitive to the length $N$ of the polygon and to solvent conditions. This "topological contribution" to the writhe distribution has a value that is consistent with that of ideal knots. The standard deviation of the writhe increases approximately as $\sqrt{N}$ in both regimes and this constitutes a geometrical contribution to the writhe. If the sum over all knot types is considered, the scaling of the standard deviation changes, for compact polygons, to $\sim N^{0.6}$. We argue that this difference between the two regimes can be ascribed to the topological contribution to the writhe that, for compact chains, overwhelms the geometrical one thanks to the presence of a large population of complex knots at relatively small values of $N$. For polygons with fixed writhe we find that the knot distribution depends on the chosen writhe, with the occurrence of achiral knots being considerably suppressed for large writhe. In general, the occurrence of a given knot thus depends on a nontrivial interplay between writhe, chain length, and solvent conditions.Comment: 10 pages, accepted in J.Chem.Phy

Linking in domain-swapped protein dimers

The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, make such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter $G'$, termed Gaussian entanglement, is strongly correlated with the linking number. Based on $110$ non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with $|G'| > 1$. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.Comment: v2: some new paragraphs and new abstrac

A Lattice Boltzmann Model of Binary Fluid Mixture

We introduce a lattice Boltzmann for simulating an immiscible binary fluid mixture. Our collision rules are derived from a macroscopic thermodynamic description of the fluid in a way motivated by the Cahn-Hilliard approach to non-equilibrium dynamics. This ensures that a thermodynamically consistent state is reached in equilibrium. The non-equilibrium dynamics is investigated numerically and found to agree with simple analytic predictions in both the one-phase and the two-phase region of the phase diagram.Comment: 12 pages + 4 eps figure

Exploring the correlation between the folding rates of proteins and the entanglement of their native states

The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native state of the protein. Contact order is related to the average length of the main chain loops formed by amino acids which are in contact. Here we argue that folding kinetics can be influenced also by the entanglement that loops may undergo within the overall three dimensional protein structure. In order to explore such possibility, we introduce a novel descriptor, which we call "maximum intrachain contact entanglement". Specifically, we measure the maximum Gaussian entanglement between any looped portion of a protein and any other non-overlapping subchain of the same protein, which is easily computed by discretized line integrals on the coordinates of the $C_{\alpha}$ atoms. By analyzing experimental data sets of two-state and multistate folders, we show that also the new index is a good predictor of the folding rate. Moreover, being only partially correlated with previous methods, it can be integrated with them to yield more accurate predictions.Comment: 8 figures. v2: new titl

Zipping and collapse of diblock copolymers

Using exact enumeration methods and Monte Carlo simulations we study the phase diagram relative to the conformational transitions of a two dimensional diblock copolymer. The polymer is made of two homogeneous strands of monomers of different species which are joined to each other at one end. We find that depending on the values of the energy parameters in the model, there is either a first order collapse from a swollen to a compact phase of spiral type, or a continuous transition to an intermediate zipped phase followed by a first order collapse at lower temperatures. Critical exponents of the zipping transition are computed and their exact values are conjectured on the basis of a mapping onto percolation geometry, thanks to recent results on path-crossing probabilities.Comment: 12 pages, RevTeX and 14 PostScript figures include