Force spectroscopy of polymer desorption: theory and molecular dynamics simulations.

Forced detachment of a single polymer chain, strongly adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics (MD) simulations with a Langevin thermostat. The suggested approach makes it possible to go beyond the limitations of the conventional Bell-Evans model. We observe a series of characteristic force spikes when the pulling force is measured against the cantilever displacement during detachment at constant velocity vc (displacement control mode) and find that the average magnitude of this force increases as vc increases. The probability distributions of the pulling force and the end-monomer distance from the surface at the moment of the final detachment are investigated for different adsorption energies ε and pulling velocities vc. Our extensive MD simulations validate and support the main theoretical findings. Moreover, the simulations reveal a novel behavior: for a strong-friction and massive cantilever the force spike pattern is smeared out at large vc. As a challenging task for experimental bio-polymer sequencing in future we suggest the fabrication of a stiff, super-light, nanometer-sized AFM probe.

Polymer translocation through a nanopore: a showcase of anomalous diffusion.

We investigate the translocation dynamics of a polymer chain threaded through a membrane nanopore by a chemical potential gradient that acts on the chain segments inside the pore. By means of diverse methods (scaling theory, fractional calculus, and Monte Carlo and molecular dynamics simulations), we demonstrate that the relevant dynamic variable, the transported number of polymer segments, s(t), displays an anomalous diffusive behavior, both with and without an external driving force being present. We show that in the absence of drag force the time tau, needed for a macromolecule of length N to thread from the cis into the trans side of a cell membrane, scales as tauN(2/alpha) with the chain length. The anomalous dynamics of the translocation process is governed by a universal exponent alpha= 2/(2nu + 2 - gamma(1)), which contains the basic universal exponents of polymer physics, nu (the Flory exponent) and gamma(1) (the surface entropic exponent). A closed analytic expression for the probability to find s translocated segments at time t in terms of chain length N and applied drag force f is derived from the fractional Fokker-Planck equation, and shown to provide analytic results for the time variation of the statistical moments and . It turns out that the average translocation time scales as tau proportional, f(-1)N(2/alpha-1). These results are tested and found to be in perfect agreement with extensive Monte Carlo and molecular dynamics computer simulations.

Directed polymers with constrained winding angle.

In this paper we study from a nonperturbative point of view the entanglement of two directed polymers subjected to repulsive interactions given by a Dirac delta-function potential. An exact formula of the so-called second moment of the winding angle is derived. This result is used to provide a thorough analysis of entanglement phenomena in the classical system of two polymers subjected to repulsive interactions and related problems. No approximation is made in treating the constraint on the winding angle and the repulsive forces. In particular, we investigate how repulsive forces influence the entanglement degree of the two-polymer system. In the limit of ideal polymers, in which the interactions are switched off, we show that our results are in agreement with those of previous works.

Localization of a multiblock copolymer at a selective interface: scaling predictions and Monte Carlo verification.

We investigate the localization of a hydrophobic-polar regular copolymer at a selective solvent-solvent interface with emphasis on the impact of block length M on the copolymer behavior. The considerations are based on simple scaling arguments and use the mapping of the problem onto a homopolymer adsorption problem. The resulting scaling relations treat the gyration radius of the copolymer chain perpendicular and parallel to the interface in terms of chain length N and block size M, as well as the selectivity parameter chi. The scaling relations differ for the case of weak and strong localization. In the strong localization limit a scaling relation for the lateral diffusion coefficient D( parallel) is also derived. We implement a dynamic off-lattice Monte Carlo model to verify these scaling predictions. For chain lengths in a wide range (32

Localization and freezing of a Gaussian chain in a quenched random potential.

The Gaussian chain in a quenched random potential (which is characterized by the disorder strength Delta) is investigated in the d-dimensional space by the replicated variational method. The general expression for the free energy within so-called one-step-replica symmetry breaking (1-RSB) scenario has been systematically derived. We have shown that the replica symmetrical (RS) limit of this expression can describe the chain center-of-mass localization and collapse. The critical disorder when the chain becomes localized scales as Delta(c) approximately b(d)N(-2+d/2) (where b is the length of the Kuhn segment length and N is the chain length) whereas the chain gyration radius R(g) approximately b(b(d)/Delta)(1/(4-d)). The freezing of the internal degrees of freedom follows to the 1-RSB-scenario and is characterized by the beads localization length D(2). It was demonstrated that the solution for D(2) appears as a metastable state at Delta=Delta(A) and behaves similarly to the corresponding frozen states in heteropolymers or in p-spin random spherical model.