arXiv subjects

A. L. Stella

Publications and source records attributed to A. L. Stella.

At least 19 recordsLinked to original sources

arXiv2011

Topological signatures of globular polymers

Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots controls the equilibrium statistics. With slipping link the ring length is divided between the loops according to a simple law, but with unexpectedly large fluctuations. These are suppressed only for unknotted loops, whose length distribution shows always a fast power law decay. We also discover and explain a topological effect interfering with that of surface tension in the globule translocation through a membrane nanopore.

cond-mat.soft↗

arXiv2007

Knot localization in adsorbing polymer rings

We study by Monte Carlo simulations a model of knotted polymer ring adsorbing onto an impenetrable, attractive wall. The polymer is described by a self-avoiding polygon (SAP) on the cubic lattice. We find that the adsorption transition temperature, the crossover exponent $ϕ$ and the metric exponent $ν$, are the same as in the model where the topology of the ring is unrestricted. By measuring the average length of the knotted portion of the ring we are able to show that adsorbed knots are localized. This knot localization transition is triggered by the adsorption transition but is accompanied by a less sharp variation of the exponent related to the degree of localization. Indeed, for a whole interval below the adsorption transition, one can not exclude a contiuous variation with temperature of this exponent. Deep into the adsorbed phase we are able to verify that knot localization is strong and well described in terms of the flat knot model.

cond-mat.soft↗

arXiv2007

Ranking knots of random, globular polymer rings

An analysis of extensive simulations of interacting self-avoiding polygons on cubic lattice shows that the frequencies of different knots realized in a random, collapsed polymer ring decrease as a negative power of the ranking order, and suggests that the total number of different knots realized grows exponentially with the chain length. Relative frequencies of specific knots converge to definite values because the free energy per monomer, and its leading finite size corrections, do not depend on the ring topology, while a subleading correction only depends on the crossing number of the knots.

cond-mat.stat-mech↗

arXiv2006

On the size of knots in ring polymers

We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the number of steps over which the knot ``spreads'' in a given configuration. An analysis of extensive Monte Carlo data in equilibrium shows that the probability distribution of l as a function of N obeys a scaling of the form p(l,N) ~ l^(-c) f(l/N^D), with c ~ 1.25 and D ~ 1. Both D and c could be independent of knot type. As a consequence, the knot is weakly localized, i.e. ~ N^t, with t=2-c ~ 0.75. For a ring with fixed knot type, weak localization implies the existence of a peculiar characteristic length l^(nu) ~ N^(t nu). In the scaling ~ N^(nu) (nu ~0.58) of the radius of gyration of the whole ring, this length determines a leading power law correction which is much stronger than that found in the case of unrestricted topology. The existence of such correction is confirmed by an analysis of extensive Monte Carlo data for the radius of gyration. The collapsed regime is studied by introducing in the model sufficiently strong attractive interactions for nearest neighbor sites visited by the self-avoiding polygon. In this regime knot length determinations can be based on the entropic competition between two knotted loops separated by a slip link. These measurements enable us to conclude that each knot is delocalized (t ~ 1).

cond-mat.stat-mech↗

arXiv2005

Precise toppling balance, quenched disorder, and universality for sandpiles

A single sandpile model with quenched random toppling matrices captures the crucial features of different models of self-organized criticality. With symmetric matrices avalanche statistics falls in the multiscaling BTW universality class. In the asymmetric case the simple scaling of the Manna model is observed. The presence or absence of a precise toppling balance between the amount of sand released by a toppling site and the total quantity the same site receives when all its neighbors topple once determines the appropriate universality class.

cond-mat.stat-mech↗

arXiv2005

What is the length of a knot in a polymer?

We give statistical definitions of the length, l, of a loose prime knot tied into a long, fluctuating ring macromolecule. Monte Carlo results for the equilibrium, good solvent regime show that < l > ~ N^t, where N is the ring length and t ~ 0.75 is independent of the knot topology. In the collapsed regime below the theta temperature, length determinations based on the entropic competition of different knots within the same ring show delocalization (t~1).

cond-mat.stat-mech↗

arXiv2004

A scale-free network hidden in the collapsing polymer

We show that the collapsed globular phase of a polymer accommodates a scale-free incompatibility graph of its contacts. The degree distribution of this network is found to decay with the exponent $γ= 1/(2-c)$ up to a cut-off degree $d_c \propto L^{2-c}$, where $c$ is the loop exponent for dense polymers ($c=11/8$ in two dimensions) and $L$ is the length of the polymer. Our results exemplify how a scale-free network (SFN) can emerge from standard criticality.

cond-mat.stat-mech↗

arXiv2003

Pseudoknots in a Homopolymer

After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the number of pseudoknots at different temperature regimes in two and three dimensions. Although the total number of pseudoknots is extensive at all temperatures, we find that the number of pseudoknots forming between the two halves of the chain diverges logarithmically at (in both dimensions) and below (in 2d only) the theta-temparature. We later introduce a simple model that is sensitive to pseudoknot formation during collapse. The resulting phase diagram involves swollen, branched and collapsed homopolymer phases with transitions between each pair.

cond-mat.stat-mech↗

arXiv2003

RNA denaturation: excluded volume, pseudoknots and transition scenarios

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.

cond-mat.soft↗

arXiv2002

The polymer theta-point as a knot delocalisation transition

We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localised in the high temperature swollen regime, but become delocalised in the low temperature globular phase. Precisely at the collapse transition, the knots are weakly localised. Some of our results can be interpreted in terms of the theory of polymer networks, which allows to conjecture exact exponents for the knot length probability distributions.

cond-mat.soft↗

arXiv2002

Inter-strand distance distribution of DNA near melting

The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes self-avoiding interactions. At the transition temperature and for a large distance r the distribution decays as 1/r^κwith κ=1+(c-2)/ ν. Here νis the self-avoiding walk correlation length exponent and c is the exponent associated with the entropy of an open loop in the chain. Results for the distribution function just below the melting point are also presented. Numerical simulations which fully take into account the self-avoiding interactions are in good agreement with the scaling approach.

cond-mat.stat-mech↗

arXiv2002

Self-organized random walks and stochastic sandpile: From linear to branched avalanches

In a model of self-organized criticality unstable sites discharge to just one of their neighbors. For constant discharge ratio $α$ and for a certain range of values of the input energy, avalanches are simple branchless Pólya random walks, and their scaling properties can be derived exactly. If $α$ fluctuates widely enough, avalanches become branched, due to multiple discharges, and behave like those of the stochastic sandpile. At the threshold for branched behaviour, peculiar scaling and anomalous diffusive transport are observed.

cond-mat.stat-mech↗

arXiv2002

Topological and geometrical entanglement in a model of circular DNA undergoing denaturation

The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the linking number to fluctuate freely in equilibrium we see that the linking probability undergoes an abrupt variation (first-order) at the denaturation transition, and stays close to 1 in the whole native phase. The average linking number is almost zero in the denatured phase and grows as the square root of the chain length, N, in the native phase. The writhe of the two strands grows as the square root of N in both phases.

cond-mat.stat-mech↗

arXiv1999

Adsorption-like Collapse of Diblock Copolymers

A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive MC simulations in two and three dimensions. In the former case, an identification with the statistical geometry of suitable percolation paths allows to predict that the number of contacts between the blocks grows like $N^{9/16}$. In the compact phase the blocks are mixed and, in two dimensions, also zipped, in such a way to form a spiral, double chain structure.

cond-mat.soft↗

arXiv1999

Boundary Spatiotemporal Correlations in a Self-Organized Critical Model of Punctuated Equilibrium

In a semi-infinite geometry, a 1D, M-component model of biological evolution realizes microscopically an inhomogeneous branching process for $M \to \infty$. This implies in particular a size distribution exponent $τ'=7/4$ for avalanches starting at a free end of the evolutionary chain. A bulk--like behavior with $τ'=3/2$ is restored if `conservative' boundary conditions strictly fix to its critical, bulk value the average number of species directly involved in an evolutionary avalanche by the mutating species located at the chain end. A two-site correlation function exponent ${τ_R}'=4$ is also calculated exactly in the `dissipative' case, when one of the points is at the border. These results, together with accurate numerical determinations of the time recurrence exponent $τ_{first}'$, show also that, no matter whether dissipation is present or not, boundary avalanches have the same space and time fractal dimensions as in the bulk, and their distribution exponents obey the basic scaling laws holding there.

cond-mat.stat-mech↗

arXiv1999

Polymer Adsorption on Fractal Walls

Polymer adsorption on fractally rough walls of varying dimensionality is studied by renormalization group methods on hierarchical lattices. Exact results are obtained for deterministic walls. The adsorption transition is found continuous for low dimension $d_w$ of the adsorbing wall and the corresponding crossover exponent $ϕ$ monotonically increases with $d_w$, eventually overcoming previously conjectured bounds. For $d_w$ exceeding a threshold value $d_w^*$, $ϕ$ becomes 1 and the transition turns first--order. $d_w^*>d_{saw}$, the fractal dimension of the polymer in the bulk. An accurate numerical approach to the same problem with random walls gives evidence of the same scenario.

cond-mat.stat-mech↗

arXiv1998

Theta-point universality of polyampholytes with screened interactions

By an efficient algorithm we evaluate exactly the disorder-averaged statistics of globally neutral self-avoiding chains with quenched random charge $q_i=\pm 1$ in monomer i and nearest neighbor interactions $\propto q_i q_j$ on square (22 monomers) and cubic (16 monomers) lattices. At the theta transition in 2D, radius of gyration, entropic and crossover exponents are well compatible with the universality class of the corresponding transition of homopolymers. Further strong indication of such class comes from direct comparison with the corresponding annealed problem. In 3D classical exponents are recovered. The percentage of charge sequences leading to folding in a unique ground state approaches zero exponentially with the chain length.

cond-mat.soft↗

arXiv1998

Rare events and breakdown of simple scaling in the Abelian sandpile

Due to intermittency and conservation, the Abelian sandpile in 2D obeys multifractal, rather than finite size scaling. In the thermodynamic limit, a vanishingly small fraction of large avalanches dominates the statistics and a constant gap scaling is recovered in higher moments of the toppling distribution. Thus, rare events shape most of the scaling pattern and preserve a meaning for effective exponents, which can be determined on the basis of numerical and exact results.

cond-mat.stat-mech↗