Attraction between like-charged walls: Short-ranged simulations using local molecular field theory.

Effective attraction between like-charged walls mediated by counterions is studied using local molecular field (LMF) theory. Monte Carlo simulations of the "mimic system" given by LMF theory, with short-ranged "Coulomb core" interactions in an effective single particle potential incorporating a mean-field average of the long-ranged Coulomb interactions, provide a direct test of the theory, and are in excellent agreement with more complex simulations of the full Coulomb system by Moreira and Netz [Eur. Phys.

Structure of nonuniform hard sphere fluids from shifted linear truncations of functional expansions.

Percus showed that approximate theories for the structure of nonuniform hard sphere fluids can be generated by linear truncations of functional expansions of the nonuniform density rho(r) about that of an appropriately chosen uniform system. We consider the most general such truncation, which we refer to as the shifted linear response (SLR) equation, where the density response rho(r) to an external field phi(r) is expanded to linear order at each r about a different uniform system with a locally shifted chemical potential. Special cases include the Percus-Yevick (PY) approximation for nonuniform fluids, with no shift of the chemical potential, and the hydrostatic linear response (HLR) equation, where the chemical potential is shifted by the local value of phi(r).

Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions.

Strong, short-ranged positional correlations involving counterions can induce a net attractive force between negatively charged strands of DNA and lead to the formation of ion pairs in dilute ionic solutions. However, the long range of the Coulomb interactions impedes the development of a simple local picture. We address this general problem by mapping the properties of a nonuniform system with Coulomb interactions onto those of a simpler system with short-ranged intermolecular interactions in an effective external field that accounts for the averaged effects of appropriately chosen long-ranged and slowly varying components of the Coulomb interactions.

Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor.

Conformational transitions underlie the function of many biomolecular systems. Resolving intermediate structural changes, however, is challenging for both experiments and all-atom simulations because the duration of transitions is short relative to the lifetime of the stable species. Simplified descriptions based on a single experimental structure, such as elastic network models or Gō models, are not immediately applicable.