Ref HAL: hal-00702529_v1
Ref Arxiv: 1203.0271
DOI: 10.1209/0295-5075/98/38002
WoS: 000304389300038
Ref. & Cit.: NASA ADS
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12 Citations
Résumé:

The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a bending modulus which depends on the base-pair state, with double-strand DNA (dsDNA) segments being 50 times stiffer than ssDNA ones. For DNA lengths from N=20 to 100 base-pairs (bp) and initial bubble sizes of N-6 bp, long closure times of 0.1 to 4 microseconds are found, following a scaling law in N^2.4. The bubble starts to close by a fast zipping which stops when the bubble reaches a highly bent metastable state of length around 10 bp. The limiting final step to complete closure is controlled by the dsDNA "arms" rotational diffusion, with closure occurring once they are nearly aligned. The central role of chain bending, which cannot be accounted for in one-dimensional models, is thus illuminated.

Commentaires: 6 pages, 7 figures

Ref HAL: hal-00682155_v1
DOI: 10.1021/jp2078924
WoS: 000298978700090
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6 Citations
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The distribution of water and ions in nanoporous membranes, in particular close to their surfaces with external reservoirs, is investigated by means of molecular dynamics (MD) simulations using classical polarizable force fields. A sodium iodide (NaI) aqueous solution is considered in uncharged weakly hydrophilic (WH) and highly hydrophilic (HH) nanoporous materials modeled by a single truncated nanopore in contact with two reservoirs. In the inner part of the nanopore, the spatial distribution of water and ions is obtained by coupling semi-infinitesimal longitudinal and semi-infinitesimal radial descriptions. In the HH material, in contrast with the WH material, species are no longer uniformly distributed in the inner nanopore and water molecules are distributed in a nearly frozen axially periodic corona-like structure which leads to the formation of ionic tunnels. In the reservoirs, water molecules and ions attracted by the membrane surface create a necking of the confined solution which acts as a barrier at the entrance of the nanopore. In the WH nanopore subsurface, close to the surface of the membrane, the species distribution is analogous to the interface distribution between an aqueous electrolyte solution and air. In the HH nanopore subsurface, this distribution is modulated by the water corona-like structure. These results provide useful information for predicting properties of nanoporous membranes, in particular the drastic reduction of diffusion coefficients in HH materials, and give a guide to designing synthetic membranes for applications in nanofiltration, etc.

Ref HAL: hal-00809039_v1
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Ref HAL: hal-00735490_v1
PMID 21341868
DOI: 10.1063/1.3526940
WoS: 000287506000048
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26 Citations
Résumé:

A field theoretic variational approach is introduced to study ion penetration into water-filled cylindrical nanopores in equilibrium with a bulk reservoir [S. Buyukdagli, M. Manghi, and J. Palmeri, Phys. Rev. Lett. 105, 158103 (2010)]. It is shown that an ion located in a neutral pore undergoes two opposing mechanisms: (i) a deformation of its surrounding ionic cloud of opposite charge, with respect to the reservoir, which increases the surface tension and tends to exclude ions from the pore, and (ii) an attractive contribution to the ion self-energy due to the increased screening with ion penetration of the repulsive image forces associated with the dielectric jump between the solvent and the pore wall. For pore radii around 1 nm and bulk concentrations lower than 0.2 mol/l, this mechanism leads to a first-order phase transition, similar to capillary "evaporation," from an ionic-penetration state to an ionic-exclusion state. The discontinuous phase transition exists within the biological concentration range (∼0.15 mol/l) for small enough membrane dielectric constants (εm < 5). In the case of a weakly charged pore, counterion penetration exhibits a nonmonotonic behavior and is characterized by two regimes: at low reservoir concentrations or small pore radii, coions are excluded and counterions enter the pore to enforce electroneutrality; dielectric repulsion (image forces) remain strong and the counterion partition coefficient decreases with increasing reservoir concentration up to a characteristic value. For larger reservoir concentrations, image forces are screened and the partition coefficient of counterions increases with the reservoir concentration, as in the neutral pore case. Large surface charge densities (>2 × 10−3 e/nm2) suppress the discontinuous transition by reducing the energy barrier for ion penetration and shifting the critical point toward very small pore sizes and reservoir concentrations. Our variational method is also compared to a previous self-consistent approach and yields important quantitative corrections. The role of the curvature of dielectric interfaces is highlighted by comparing ionic penetration into slit and cylindrical pores. Finally, a charge regulation model is introduced in order to explain the key effect of pH on ionic exclusion and explain the origin of observed time-dependent nanopore electric conductivity fluctuations and their correlation with those of the pore surface charge.

Ref HAL: hal-00809029_v1
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Ref HAL: hal-00439696_v1
PMID 19810684
DOI: 10.1021/la9028723
WoS: 000274342200059
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35 Citations
Résumé:

The thin active layer (TAL) of seven nanofiltration (NF) membranes was studied using differential scanning calorimetry, and the membranes were classified into two groups according to the polymer physical state (amorphous or semicrystalline). NF membrane performance in terms of permeate volume flux density and rejection OF neutral solutes was investigated in temperature cycles. The modeling of rejection using a hindered transport theory showed irreversible and opposite pore size changes for the two groups of NF membranes when the maximum operating temperature of the cycle exceeded the glass-transition temperature of the TAL. A mechanism of pore deformation is proposed to explain the variation of the solute transport properties as a function of the temperature and the polymer physical state in the TAL.

Ref HAL: hal-00559645_v1
Ref Arxiv: 1004.1816
Ref. & Cit.: NASA ADS
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Résumé:

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 repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.