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We employ a field-theoretical variational approach to study the behavior of ionic solutions in nanopores.

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DOI: 10.1039/c7nr02976d
WoS: WOS:000408435400019
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13 Citations
Résumé:

Ionic transport through single-walled carbon nanotubes (SWCNTs) is promising for many applications but remains both experimentally challenging and highly debated. Here we report ionic current measurements through microfluidic devices containing one or several SWCNTs of diameter of 1.2 to 2 nm unexpectedly showing a linear or a voltage-activated I-V dependence. Transition from an activated to a linear behavior, and stochastic fluctuations between different current levels were notably observed. For linear devices, the high conductance confirmed with different chloride salts indicates that the nanotube/water interface exhibits both a high surface charge density and flow slippage, in agreement with previous reports. In addition, the sublinear dependence of the conductance on the salt concentration points toward a charge-regulation mechanism. Theoretical modelling and computer simulations show that the voltage-activated behavior can be accounted for by the presence of local energy barriers along or at the ends of the nanotube. Raman spectroscopy reveals strain fluctuations along the tubes induced by the polymer matrix but displays insufficient doping or variations of doping to account for the apparent surface charge density and energy barriers revealed by ion transport measurements. Finally, experimental evidence points toward environment-sensitive chemical moieties at the nanotube mouths as being responsible for the energy barriers causing the activated transport of ions through SWCNTs within this diameter range.

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Ref Arxiv: 1707.01373
DOI: 10.1088/1367-2630/aaad39
WoS: 000428767700002
Ref. & Cit.: NASA ADS
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4 Citations
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The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Commentaires: 14 pages, 7 figures

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Ref Arxiv: 1702.07372
DOI: 10.1103/PhysRevLett.119.028101
WoS: 000405367800016
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14 Citations
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Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component machinery, fueled by adenosine triphosphate, called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation, and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a nonlinear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and traveling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.

Commentaires: 6 pages, 3 figures

Ref HAL: hal-01950249_v1
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Bacteria, a few μm in length, have the feature to store the genome in a subvolume of the cell without membrane. The bacterial cell cycle relies on a series of essential processes such as DNA replication, transcription and segregation. The mechanisms driving segregation of the genome are still unclear, mainly because the processes overlap in time and take place in the same cellular compartment. The active ParABS partition system is the only type known on chromosomes and is prevalent on low-copy number plasmids,namely the F-plasmid involved in bacterial resistance to antibiotics. ParABS is composed of three components: the proteins ParA and ParB, respectively a molecular motor (ATPase) and a binding protein, and parS, a sequence of specific binding sites. We describe the organization and architecture of the partition complex. Our model is supported by experimental data from ChIP-sequencing (LMGM, Toulouse) and super resolution microscopy techniques (CBS, Montpellier).

Ref HAL: hal-01950212_v1
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We present experimental and theoretical results for the transport of ions and molecules inside carbon nanotubes.