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We model the ParABS system, which is a bacterial DNA Segregation Apparatus.

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We present a modeling study of the electrical conductivity of charged nanopores.

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Nous présentons les activités en 2016 du Projet intégré « ADN et Génomes » du LabEx NUMEV.

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Nous développons une approche de modélisation pluridisciplinaire, de type génomique physique, dans le but de comprendre les mécanismes de la dynamique active des complexes intracellulaires protéines-ADN bactériens. Son but est d’unifier quantitativement, sur la base de méthodes de physique statistique, l’information provenant des expériences de séquençage à haut débit avec les données de l’imagerie moderne de super-résolution.

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DOI: 10.1016/j.bpj.2015.11.3504
WoS: 000375143200296
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In the area of nanopore technology, detection methods are based on the recorded electrical signal induced by ionic transport through the nanopore.This signal also is often used to determine the nanopore diameter. Thus fundamental understanding of ionic transport at the nanoscale is essential, because ions do not in general exhibit bulk-like behavior. Indeed, at low salt concentration, the conductance-concentration relation does not follow a bulk-like linear law. In addition, for small nanopores, surface effects can prevail over bulk transport. In order to illustrate this phenomenon, we have tailored high aspect ratio (conical and cylindrical), putatively uncharged nanopores using tracketching on PET Film and atomic layer deposition technique. Starting from experimental results, we will discuss different approaches to fitting the data, including a simple phenomenological model, commonly used to determine nanopore diameter, and a more sophisticated mesoscopic model based on the space charge model. Application of the mesoscopic model leads us to conclude that, surprisingly, a weak surface charge density is needed to fit the transport model to the experimental data. To go further, molecular dynamic simulations were also performed on a system modeled to resemble as closely as possible the experimental one. From different nanopore geometries and the adsorption of hydrophibic polypeptides, we will attempt to explain the origin of the weak surfacecharge.

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DOI: 10.1063/1.4959034
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We employ a field-theoretical variational approach to study the behavior of ionic solutions in the grand canonical ensemble. To describe properly the hardcore interactions between ions, we use a cutoff in Fourier space for the electrostatic contribution of the grand potential and the Carnahan-Starling equation of state with a modified chemical potential for the pressure one. We first calibrate our method by comparing its predictions at room temperature with Monte Carlo results for excess chemical potential and energy. We then validate our approach in the bulk phase by describing the classical “ionic liquid-vapor” phase transition induced by ionic correlations at low temperature, before applying it to electrolytes at room temperature confined to nanopores embedded in a low dielectric medium and coupled to an external reservoir of ions. The ionic concentration in the nanopore is then correctly described from very low bulk concentrations, where dielectric exclusion shifts the transition up to room temperature for sufficiently tight nanopores, to high concentrations where hardcore interactions dominate which, as expected, modify only slightly this ionic “capillary evaporation.”