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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 non-zero torsional modulus in the duplex state, $\kappa_\phi=$200 to 300 kT. For DNAs of lengths N=40 to 100 base-pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100 microseconds are found. The bubble starts winding from both ends until it reaches a 10 bp metastable state. The final closure is limited by three competing mechanisms depending on $\kappa_\phi$ and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this latter temperature activated mechanism, yielding for the first time a good quantitative agreement with experiments.

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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 liquids with variable molecular quadrupole moments that interpolates between SPC/E water and a purely dipolar liquid. We then pinpoint the essential role played by the competing multipolar contributions to the vapor-liquid and the solute-liquid interface potentials in determining an important ion-specific direct electrostatic contribution to the ionic solvation free energy for SPC/E water---dominated by the quadrupolar and dipolar contributions---beyond the dominant polarization one. Our results show that the influence of the vapor-liquid interfacial potential on ion solvation is strongly reduced due to the strong partial cancellation brought about by the competing solute-liquid interface potential.

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The use of nanofiltration as a pretreatment step in a zero rejection process was investigated. Nanoflux, a nanofiltration simulation software, was used to predict the rejection of Co2+ and Ni2+ from a salty multi-element matrix whose concentration is similar to seawater. Orientation simulations prior to filtration experiments were made with Nanoflux in order to predict ionic rejections. Previously, the multi-element matrix solution speciation was studied by JChess. It was shown that the effective membrane charge and the effective membrane thickness, adjusted through the filtration of a single salt NaNO3 solution, could be used to predict the ionic rejections of the multi-element solution for two commercial nanofiltration membranes. The elevated concentration of NaNO3 in the multi-electrolyte solution did not reduce the high ionic selectivity of divalent ions. Predicted values were in good agreement with experimental results at neutral pH of the multi-electrolyte solution.

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A study has been undertaken of an advanced wastewater treatment approach using polymer nanofiltration membranes, in an attempt to obtain water of sufficient quality to allow it to be reused in the same production process or, alternatively, to be discharged without any problems. The study has initially focused on the removal of organic matter (reduction of COD) and the most representative ions present in the wastewater, such as Na+, Mg2+, Cl-, and SO42-. In a first part of the study, with a view to optimising the experimental phase, a simulation has been performed of the nanofiltration process using the NanoFlux software. Among other things, the simulation allows the most suitable membranes to be selected as a function of the permeate flow rate and desired level of retention in the substances to be removed. The subsequent experimentation was carried out in a laboratory tangential filtration system that works with flat membranes. It was found that retention values of about 90% were obtained for the studied substances, with a good permeate flow rate, using low operating pressures. These results demonstrate the feasibility of the studied technology and its potential as a treatment for improving ceramic industry wastewater quality.

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en ligne sur UM2 WebTV http://www.webtv.univ-montp2.fr/14478/nanoflux-un-logiciel-de-prediction-des-performances-des-membranes-de-nanoflitration-nf/

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Single-molecule experiments on double-stranded B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. The nature and the critical forces of these transitions depend on DNA base sequence, loading rate, salt conditions and temperature. It has been proposed that the first transition, at forces of 60-80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single-stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). In an attempt to propose a coherent picture compatible with this variety of experimental observations, we derive an analytical formula using a coupled discrete worm-like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connection with previous fitting parameter values for denaturation profiles. Our results are summarized as follows: i) ssDNA is fitted, using an analytical formula, over a nano-Newton range with only three free parameters, the contour length, the bending modulus and the monomer size; ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; v) this formula fits perfectly well poly(dG-dC) and λ-DNA force-extension curves with consistent parameter values; vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges. This relatively simple model might allow one to further study quantitatively the influence of salt concentration and base-pairing interactions on DNA force-induced transitions.