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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. J. E 8, 33 (2002)]. A simple, generally applicable criterion to determine the consistency parameter sigma(min) needed for accurate use of the LMF theory is presented.

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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. The remaining short-ranged components combine with the other molecular core interactions and strongly affect pair correlations in dense or strongly coupled systems. We show that pair correlation functions in the effective short-ranged system closely resemble those in the uniform primitive model of ionic solutions and illustrate the formation of ion pairs and clusters at low densities. The theory accurately describes detailed features of the effective attraction between two equally charged walls at strong coupling and intermediate separations of the walls. Analytical results for the minimal coupling strength needed to get any attraction and for the separation at which the attractive force is a maximum are presented.

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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 Go models, are not immediately applicable. Here, we develop a general method that combines multiple coarse-grained models to capture slow conformational transitions. Individually, each model describes one of the experimental structures; together, they approximate the complete energy surface. We demonstrate the method for the helix-to-sheet transition in Arc repressor N11L. We find that the transition involves the partial unfolding of the switch region, and rapid refolding into the alternate structure. Transient local unfolding is consistent with the low hydrogen exchange protection factors of the switch region. Also in agreement with experiment, the isomerization occurs independently of the global folding/dimerization transition.

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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). The HLR equation gives exact results for very slowly varying phi(r) and reduces to the PY approximation for hard core phi(r), where generally accurate results are found. We show that a truncated expansion about the bulk density (the PY approximation) also gives exact results for localized fields that are nonzero only in a "tiny" region whose volume V(phi) can accommodate at most one particle. The SLR equation can also exactly describe a limit where the fluid is confined by hard walls to a very narrow slit. This limit can be related to the localized field limit by a simple shift of the chemical potential, leading to an expansion about the ideal gas. We then try to develop a systematic way of choosing an optimal local shift in the SLR equation for general phi(r) by requiring that the predicted rho(r) is insensitive to small variations about the appropriate local shift, a property that the exact expansion to all orders would obey. The resulting insensitivity criterion (IC) gives a theory that reduces to the HLR equation for slowly varying phi(r) and is much more accurate than HLR both for very narrow slits, where the IC agrees with exact results, and for fields confined to "tiny" regions, where the IC gives very accurate (but not exact) results. However, the IC is significantly less accurate than the PY and HLR equations for single hard core fields. Only a small change in the predicted reference density is needed to correct this remaining limit.