John Palmeri

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We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri et al 2007 Phys. Rev. Lett. 99 088103). Our discrete helical wormlike chain model takes explicitly into account the three elastic degrees of freedom, namely stretching, bending and torsion of the polymer. By integrating out these external variables, the(More)
A statistical model of homopolymer DNA, coupling internal base-pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length is deduced. The thermal denaturation transition emerges(More)
By exploring a recent model in which DNA bending elasticity, described by the wormlike chain model, is coupled to basepair denaturation, we demonstrate that small denaturation bubbles lead to anomalies in the flexibility of DNA at the nanometric scale, when confined in two dimensions (2D), as reported in atomic-force microscopy experiments. Our model yields(More)
A variational theory is developed to study electrolyte solutions, composed of interacting pointlike ions in a solvent, in the presence of dielectric discontinuities and charges at the boundaries. Three important and nonlinear electrostatic effects induced by these interfaces are taken into account: surface charge induced electrostatic field, solvation(More)
The interface between the vapor and liquid phase of quadrupolar-dipolar fluids is the seat of an electric interfacial potential whose influence on ion solvation and distribution is not yet fully understood. To obtain further microscopic insight into water specificity we first present extensive classical molecular dynamics simulations of a series of model(More)
Organic and inorganic nanoporous membranes, which are known to enhance the diffusion of certain species such as ions and to have a strong selectivity, are very attractive for nanofiltration and therapeutic applications. As a result, many experiments have been carried out to prepare and evaluate the performances of synthetic membranes that reproduce the(More)
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of broken bonds, or bubble, compared to the double stranded state, the inclusion of the molecular conformational degrees of(More)
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring freely rotating strands, with a nonzero torsional modulus in the duplex state, κ(φ)=200 to 300k(B)T. For DNAs of lengths N=40 to 100 base pairs (bps)(More)
Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric(More)
We applied an approximate analytic method, the good co-ion exclusion (GCE) approximation, to the hindered electrotransport theory describing salt and solution transport across charged nanofiltration membranes. This approximation, which should be valid at sufficiently low feed electrolyte concentration, leads to a considerable simplification of the exact(More)