Variance sum rule for entropy production.

Entropy production is the hallmark of nonequilibrium physics, quantifying irreversibility, dissipation, and the efficiency of energy transduction processes. Despite many efforts, its measurement at the nanoscale remains challenging. We introduce a variance sum rule (VSR) for displacement and force variances that permits us to measure the entropy production rate σ in nonequilibrium steady states. We first illustrate it for directly measurable forces, such as an active Brownian particle in an optical trap. We then apply the VSR to flickering experiments in human red blood cells. We find that σ is spatially heterogeneous with a finite correlation length, and its average value agrees with calorimetry measurements. The VSR paves the way to derive σ using force spectroscopy and time-resolved imaging in living and active matter.

Interacting elastic lattice polymers: a study of the free energy of globular rings.

We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and compact configurations, an essential prerequisite to study the scaling behavior of free energies. By simulating interacting self-avoiding rings at several temperatures in the collapsed phase, we estimate both the bulk and the surface free energy. Moreover from the corresponding estimate of the entropic exponent α-2 we provide evidence that, unlike for swollen and Θ-point rings, the hyperscaling relation is not satisfied for globular rings.

Nonequilibrium fluctuation-dissipation theorem and heat production.

We use a relationship between response and correlation function in nonequilibrium systems to establish a connection between the heat production and the deviations from the equilibrium fluctuation-dissipation theorem. This scheme extends the Harada-Sasa formulation [Phys. Rev. Lett. 95, 130602 (2005)], obtained for Langevin equations in steady states, as it also holds for transient regimes and for discrete jump processes involving small entropic changes. Moreover, a general formulation includes two times and the new concepts of two-time work, kinetic energy, and of a two-time heat exchange that can be related to a nonequilibrium "effective temperature." Numerical simulations of a chain of anharmonic oscillators and of a model for a molecular motor driven by adenosine triphosphate hydrolysis illustrate these points.

Unwinding relaxation dynamics of polymers.

The relaxation dynamics of a polymer wound around a fixed obstacle constitutes a fundamental instance of polymer with twist and torque, and it is also of relevance for DNA denaturation dynamics. We investigate it by simulations and Langevin equation analysis. The latter predicts a relaxation time scaling as a power of the polymer length times a logarithmic correction related to the equilibrium fluctuations of the winding angle. The numerical data support this result and show that at short times the winding angle decreases as a power law. This is also in agreement with the Langevin equation provided a winding-dependent friction is used, suggesting that such reduced description of the system captures the basic features of the problem.

Universal properties of knotted polymer rings.

By performing Monte Carlo sampling of N-steps self-avoiding polygons embedded on different Bravais lattices we explore the robustness of universality in the entropic, metric, and geometrical properties of knotted polymer rings. In particular, by simulating polygons with N up to 10(5) we furnish a sharp estimate of the asymptotic values of the knot probability ratios and show their independence on the lattice type. This universal feature was previously suggested, although with different estimates of the asymptotic values. In addition, we show that the scaling behavior of the mean-squared radius of gyration of polygons depends on their knot type only through its correction to scaling. Finally, as a measure of the geometrical self-entanglement of the self-avoiding polygons we consider the standard deviation of the writhe distribution and estimate its power-law behavior in the large N limit. The estimates of the power exponent do depend neither on the lattice nor on the knot type, strongly supporting an extension of the universality property to some features of the geometrical entanglement.

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 noninteracting 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 always shows 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.

Unwinding dynamics of double-stranded polymers.

We consider the unwinding of two lattice polymer strands of length N that are initially wound around each other in a double-helical conformation and evolve through Rouse dynamics. The problem relates to quickly bringing a double-stranded polymer well above its melting temperature, i.e., the binding interactions between the strands are neglected, and the strands separate from each other as it is entropically favorable for them to do so. The strands unwind by rotating around each other until they separate. We find that the process proceeds from the ends inward; intermediate conformations can be characterized by a tightly wound inner part, from which loose strands are sticking out, with length l∼t(0.39). The total time needed for the two strands to unwind scales as a power of N as τ(u)∼N(2.57±0.03). We present a theoretical argument, which suggests that during this unwinding process, these loose strands are far out of equilibrium.

Elastic lattice polymers.

We study a model of "elastic" lattice polymer in which a fixed number of monomers m is hosted by a self-avoiding walk with fluctuating length l . We show that the stored length density ρm≡1-/m scales asymptotically for large m as ρm=ρ∞(1-θ/m+…) , where θ is the polymer entropic exponent, so that θ can be determined from the analysis of ρm. We perform simulations for elastic lattice polymer loops with various sizes and knots, in which we measure ρm. The resulting estimates support the hypothesis that the exponent θ is determined only by the number of prime knots and not by their type. However, if knots are present, we observe strong corrections to scaling, which help to understand how an entropic competition between knots is affected by the finite length of the chain.

Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays.

Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Experiments confirm the model predictions for the intensity vs free-energy behavior. The existence of slow relaxation phenomena has important consequences for the specificity of microarrays as devices for the detection of a target sequence from a complex mixture of nucleic acids.

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.

Scale-free networks from a Hamiltonian dynamics.

Contrary to many recent models of growing networks, we present a model with fixed number of nodes and links, where a dynamics favoring the formation of links between nodes with degree of connectivity as different as possible is introduced. By applying a local rewiring move, the network reaches equilibrium states assuming broad degree distributions, which have a power-law form in an intermediate range of the parameters used. Interestingly, in the same range we find nontrivial hierarchical clustering.

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.

Interstrand 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 that includes self-avoiding interactions. At the transition temperature and for a large distance r, the distribution decays as 1/r(kappa) with kappa=1+(c-2)/nu. Here nu is 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 that fully take into account the self-avoiding interactions are in good agreement with the scaling approach.

Peculiar scaling of self-avoiding walk contacts.

The nearest neighbor contacts between the two halves of an N-site lattice self-avoiding walk offer an unusual example of scaling random geometry: for N-->infinity they are strictly finite in number but their radius of gyration R(c) is power law distributed proportional to R(-tau)(c), where tau>1 is a novel exponent characterizing universal behavior. A continuum of diverging length scales is associated with the R(c) distribution. A possibly superuniversal tau = 2 is also expected for the contacts of a self-avoiding or random walk with a confining wall.

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 diblock copolymer in two dimensions. 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 phase 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.