Nanofluidics has a very promising future owing to its numerous applications in many domains. It remains, however, very difficult to understand the basic physico-chemical principles that control the behavior of solvents confined in nanometric channels. Here, water and ion transport in carbon nanotubes is investigated using classical force field molecular dynamics simulations. By combining one single walled carbon nanotube (uniformly charged or not) with two perforated graphene sheets, we mimic single nanopore devices similar to experimental ones. The graphitic edges delimit two reservoirs of water and ions in the simulation cell from which a voltage is imposed through the application of an external electric field. By analyzing the evolution of the electrolyte conductivity, the role of the carbon nanotube geometric parameters (radius and chirality) and of the functionalization of the carbon nanotube entrances with OH or COO− groups is investigated for different concentrations of group functions.

In recent experiments, unprecedentedly large values for the conductivity of electrolytes through carbon nanotubes (CNTs) have been measured, possibly owing to flow slip and a high pore surface charge density whose origin is still unknown. By accounting for the coupling between the {quantum} CNT and the {classical} electrolyte-filled pore capacitances, we study the case where a gate voltage is applied to the CNT. The computed surface charge and conductivity dependence on reservoir salt concentration and gate voltage are intimately connected to the CNT electronic density of states. This approach provides key insight into why metallic CNTs have larger conductivities than semi-conducting ones.

Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50nm) of the 3D physical location of multiple (up to ~10^2) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr.21 obtained from multiplexed FISH methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags, aiming to unravel the chromatin conformational arrangements. We show that for any specific genomic site, there are (at least) two different conformational arrangements of chromatin, implying coexisting distinct topologies which we refer to as phase "alpha" and phase "beta". These two phases show different scaling behaviors: the former is consistent with a crumpled globule while the latter indicates a confined, but more extended conformation, as a looped domain. The identification of these distinct phases sheds light on the coexistence of multiple chromatin topologies and provides insights into the effects of cellular context and/or treatments on chromatin structure.

Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA into polypeptide sequences of amino acids. Here, by taking into account messenger RNA degradation, we model the motion of ribosomes along messenger RNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes onto messenger RNA. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the messenger RNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per messenger RNA, study the different regimes of degradation, and propose a criteria for the quality of the inverse fit. The proposed method provides a high sensitivity to the messenger RNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible messenger RNA degradation rate.

Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribosome sequencing (Ribo-Seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes into mRNA. The degradation rate is not, however, accounted for and experimental data from differentexperiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We analytically solve the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criterion for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) Ribo-Seq profiles enables us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

Le transport ultra-efficace de l'eau et des ions à l'échelle nanométrique est étudié par des simulations de dynamique moléculaire. Les nanotubes de carbone (CNTs) sont utilisés ici comme dispositifs nanofluidiques en raison de leur structure interne lisse et du compromis d'une composition très simple pour une énorme variété de propriétés. Le transport d'ions solvatés se déplaçant à l'intérieur du nanotube de carbone sous l'application d'une différence de potentiel externe a permis de mesurer le courant ionique établi à travers la zone interne du tube. Pour être le plus exhaustif possible, trois modèles d'eau populaires ont été testés pour étudier le transport ionique à l'intérieur de ce nanocanal artificiel. Les paramètres géométriques clés de la structure en carbone ont également été variés révélant une dépendance particulière de la conductance ionique à chaque paramètre étudié en accord avec le modèle théorique présenté dans cet article. Fichier révisé Version propre-Pour la mise en page Cliquez ici pour voir les références liées

The field of ion transport through carbon nanotubes (CNTs) is marked by a large variability of the ionic conductance values reported by different groups. There is also a large uncertainty concerning the relative contributions of channel and access resistances in the experimentally measured currents, both depending on experimental parameters (nanotube length and diameter). In this perspective article, we discuss the ionic conductance values reported so far in the case of 2 individual CNTs and compare them with standard nano-fluidic models considering both the access and channel resistances. With a view toward guiding experimentalists, we thus show in which conditions the access or the channel resistance can predominate in CNTs. We explain in particular that it is not justified to use phenomenological models neglecting the channel resistance in the case of micrometer-long CNTs. This comparison reveals that most experimental conductance values can be explained in the framework of current nanofluidic models by considering experimental variations of slip length and surface charge density and that just a few extraordinarily high values cannot be accounted for even using extreme parameter values. Finally, we discuss how to complete existing models and how to improve the statistical reliability of experimental data in the field.