Stability of phases of a square-well fluid within superposition approximation

A Euclidean perspective on the unfolding of azurin: chain motion

We present a new approach to visualizing and quantifying the displacement of segments of Pseudomonas aeruginosa azurin in the early stages of denaturation. Our method is based on a geometrical method developed previously by the authors, and elaborated extensively for azurin. In this study, we quantify directional changes in three α-helical regions, two regions having β-strand residues, and three unstructured regions of azurin. Snapshots of these changes as the protein unfolds are displayed and described quantitatively by introducing a scaling diagnostic. In accord with molecular dynamics simulations, we show that the long α-helix in azurin (residues 54-67) is displaced from the polypeptide scaffolding and then pivots first in one direction, and then in the opposite direction as the protein continues to unfold. The two β-strand chains remain essentially intact and, except in the earliest stages, move in tandem. We show that unstructured regions 72-81 and 84-91, hinged by β-strand residues 82-83, pivot oppositely. The region comprising residues 72-91 (40 % hydrophobic and 16 % of the 128 total residues) forms an effectively stationary region that persists as the protein unfolds. This static behavior is a consequence of a dynamic balance between the competing motion of two segments, residues 72-81 and 84-91.

Singular value decomposition of the radial distribution function for hard sphere and square well potentials

We compute the singular value decomposition of the radial distribution function g(r) for hard sphere, and square well solutions. We find that g(r) decomposes into a small set of basis vectors allowing for an extremely accurate representation at all interpolated densities and potential strengths. In addition, we find that the coefficient vectors describing the magnitude of each basis vector are well described by a low-order polynomial. We provide a program to calculate g(r) in this compact representation for the investigated parameter range.

Communication: Nonexistence of a critical point within the Kirkwood superposition approximation

An analytic argument is given to show that the application of the Kirkwood superposition approximation to the description of fluid correlation functions precludes the existence of a critical point. The argument holds irrespective of the dimension of the system and the specific form of the interaction potential and settles a long-standing controversy surrounding the nature of the critical behavior predicted within the approximation.