A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011

Forced-induced desorption of a polymer chain adsorbed on an attractive surface - Theory and Computer Experiment

We consider the properties of a self-avoiding polymer chain, adsorbed on a solid attractive substrate which is attached with one end to a pulling force. The conformational properties of such chain and its phase behavior are treated within a Grand Canonical Ensemble (GCE) approach. We derive theoretical expressions for the mean size of loops, trains, and tails of an adsorbed chain under pulling as well as values for the universal exponents which describe their probability distribution functions. A central result of the theoretical analysis is the derivation of an expression for the crossover exponent $\phi$, characterizing polymer adsorption at criticality, $\phi = \alpha -1$, which relates the precise value of $\phi$ to the exponent $\alpha$, describing polymer loop statistics. We demonstrate that $1-\gamma_{11} < \alpha < 1 + \nu$, depending on the possibility of a single loop to interact with neighboring loops in the adsorbed polymer. The universal surface loop exponent $\gamma_{11} \approx -0.39$ and the Flory exponent $\nu \approx 0.59$. We present the adsorption-desorption phase diagram of a polymer chain under pulling and demonstrate that the relevant phase transformation becomes first order whereas in the absence of external force it is known to be a continuous one. The nature of this transformation turns to be dichotomic, i.e., coexistence of different phase states is not possible. These novel theoretical predictions are verified by means of extensive Monte Carlo simulations.Comment: 24 pages, 14 figure

The escape transition of a polymer: A unique case of non-equivalence between statistical ensembles

A flexible polymer chain under good solvent conditions, end-grafted on a flat repulsive substrate surface and compressed by a piston of circular cross-section with radius L may undergo the so-called “escape transition” when the height of the piston D above the substrate and the chain length N are in a suitable range. In this transition, the chain conformation changes from a quasi-two-dimensional self-avoiding walk of “blobs” of diameter D to an inhomogeneous “flower” state, consisting of a “stem” (stretched string of blobs extending from the grafting site to the piston border) and a “crown” outside of the confining piston. The theory of this transition is developed using a Landau free-energy approach, based on a suitably defined (global) order parameter and taking also effects due to the finite chain length N into account. The parameters of the theory are determined in terms of known properties of limiting cases (unconfined mushroom, chain confined between infinite parallel walls). Due to the non-existence of a local order parameter density, the transition has very unconventional properties (negative compressibility in equilibrium, non-equivalence between statistical ensembles in the thermodynamic limit, etc.). The reasons for this very unusual behavior are discussed in detail. Using Molecular Dynamics (MD) simulation for a simple bead-spring model, with N in the range 50 $\leq$ N $\leq$ 300 , a comprehensive study of both static and dynamic properties of the polymer chain was performed. Even though for the considered rather short chains the escape transition is still strongly rounded, the order parameter distribution does reveal the emerging transition clearly. Time autocorrelation functions of the order parameter and first passage times and their distribution indicate clearly the strong slowing down associated with the chain escape. The theory developed here is in good agreement with all these simulation results