Density of states for a short overlapping-bead polymer: clues to a mechanism for helix formation?

The densities of states are evaluated for very short chain molecules made up of overlapping monomers, using a model which has previously been shown to produce helical structure. The results of numerical calculations are presented for tetramers and pentamers. We show that these models demonstrate behaviors relevant to the behaviors seen in longer, helix-forming chains, particularly "magic numbers" of the overlap parameter, where the derivatives of the densities of states change discontinuously, and a region of bimodal energy probability distributions, reminiscent of a first-order phase transition in a bulk system.

Structure and aggregation of a helix-forming polymer.

We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between intermolecular and intramolecular interactions, and the promotion or disruption of secondary structure brought on by the proximity of the two molecules. In particular, we demonstrate that proximity between two such molecules can stabilize secondary structure.

Helical structures from an isotropic homopolymer model.

We present Monte Carlo simulation results for square-well homopolymers at a series of bond lengths. Although the model contains only isotropic pairwise interactions, under appropriate conditions this system shows spontaneous chiral symmetry breaking, where the chain exists in either a left- or a right-handed helical structure. We investigate how this behavior depends upon the ratio between bond length and monomer radius.

Phase behavior and thermodynamic anomalies of core-softened fluids.

We report extensive simulation studies of phase behavior in single component systems of particles interacting via a core-softened interparticle potential. Two recently proposed examples of such potentials are considered; one in which the hard core exhibits a shoulder [Sadr-Lahijany et al., Phys.