Self-avoiding walks and manifolds in random environments

Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties

Here, we provide insights into the thermodynamic properties of A β16-21 dissociation from an amyloid fibril using all-atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers-of-mass of the A β16-21 peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard-Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A β16-21.

Simulating flexible polymers in a potential of randomly distributed hard disks

We perform equilibrium computer simulations of a two-dimensional pinned flexible polymer exposed to a quenched disorder potential consisting of hard disks. We are especially interested in the high-density regime of the disorder, where subtle structures such as cavities and channels play a central role. We apply an off-lattice growth algorithm proposed by Garel and Orland [J. Phys. A 23, L621 (1990)], where a distribution of polymers is constructed in parallel by growing each of them monomer by monomer. In addition we use a multicanonical Monte Carlo method in order to cross-check the results of the growth algorithm. We measure the end-to-end distribution and the tangent-tangent correlations. We also investigate the scaling behavior of the mean square end-to-end distance in dependence on the monomer number. While the influence of the potential in the low-density case is merely marginal, it dominates the configurational properties of the polymer for high densities.

Semiflexible polymers in a random environment

We present using simple scaling arguments and one step replica symmetry breaking a theory for the localization of semiflexible polymers in a quenched random environment. In contrast to completely flexible polymers, localization of semiflexible polymers depends not only on the details of the disorder but also on the ease with which polymers can bend. The interplay of these two effects can lead to the delocalization of a localized polymer with an increase in either the disorder density or the stiffness. Our theory provides a general criterion for the delocalization of polymers with varying degrees of flexibility and allows us to propose a phase diagram for the highly folded (localized) states of semiflexible polymers as a function of the disorder strength and chain rigidity.

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.

Polymers in long-range-correlated disorder

We study the scaling properties of polymers in a d-dimensional medium with quenched defects that have power law correlations approximately r(-a) for large separations r. This type of disorder is known to be relevant for magnetic phase transitions. We find strong evidence that this is true also for the polymer case. Applying the field-theoretical renormalization group approach we perform calculations both in a double expansion in epsilon=4-d and delta=4-a up to the one-loop order and second in a fixed dimension (d=3) approach up to the two-loop approximation for different fixed values of the correlation parameter, 2<or=a<or=3. In the latter case the numerical results need appropriate resummation. We find that the asymptotic behavior of self-avoiding walks in three dimensions and long-range-correlated disorder is governed by a set of separate exponents. In particular, we give estimates for the nu and gamma exponents as well as for the correction-to-scaling exponent omega. The latter exponent is also calculated for the general m-vector model with m=1,2,3.