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. Rev. Lett. 81, 4895 (1998)], and the other in which the softening takes the form of a linear ramp [Jagla, Phys. Rev. E 63, 061501 (2001)]. Using a combination of state-of-the-art Monte Carlo methods, we obtain the gas, liquid, and solid phase behavior of the shoulder model in two dimensions. We then focus on the thermodynamic anomalies of the liquid phase, namely, maxima in the density and compressibility as a function of temperature. Analysis of the finite-size behavior of these maxima suggests that, rather than stemming from a metastable liquid-liquid critical point, as previously supposed, they are actually induced by the quasicontinuous nature of the two dimensional freezing transition. For the ramp model in three dimensions, we confirm the existence of a stable liquid-liquid ("second") critical point occurring at higher pressure and lower temperature than the liquid-gas critical point. Both these critical points and portions of their associated coexistence curves are located to high precision. In contrast to the shoulder model, the observed thermodynamic anomalies of this model are found to be authentic, i.e., they are not engendered by an incipient new phase. We trace the locus of density and compressibility maxima, the former of which appears to terminate close to the second critical point.

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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.

Protein–nucleic acid interactions exhibit varying degrees of specificity. Relatively high affinity, sequence-specific interactions, can be studied with structure determination, but lower affinity, non-specific interactions are also of biological importance. We report simulations that predict the population of nucleic acid paths around protein surfaces, and give binding constant differences for changes in the protein scaffold. The method is applied to the non-specific component of interactions between eIF4Es and messenger RNAs that are bound tightly at the cap site. Adding a fragment of eIF4G to the system changes both the population of mRNA paths and the protein–mRNA binding affinity, suggesting a potential role for non-specific interactions in modulating translational properties. Generally, the free energy simulation technique could work in harness with characterized tethering points to extend analysis of nucleic acid conformation, and its modulation by protein scaffolds.

Recently, it has been demonstrated [Magee, Phys. Rev. Lett. 96, 207802 (2006)] that isolated square-well homopolymers can spontaneously break chiral symmetry and "freeze" into helical structures at sufficiently low temperatures. This behavior is interesting because the square-well homopolymer is itself achiral. In this work, we use event-driven molecular dynamics combined with an optimized parallel tempering scheme to study this polymer model over a wide range of parameters. We examine the conditions where the helix structure is stable and determine how the interaction parameters of the polymer govern the details of the helix structure. The width of the square well (proportional to lambda) is found to control the radius of the helix, which decreases with increasing well width until the polymer forms a coiled sphere for sufficiently large wells. The helices are found to be stable for only a "window" of molecular weights. If the polymer is too short, the helix will not form. If the polymer is too long, the helix is no longer the minimum energy structure, and other folded structures will form. The size of this window is governed by the chain stiffness, which in this model is a function of the ratio of the monomer size to the bond length. Outside this window, the polymer still freezes into a locked structure at low temperature; however, unless the chain is sufficiently stiff, this structure will not be unique and is similar to a glassy state.