In bacteria, faithful DNA segregation of chromosomes and plasmids is mainly mediated by ParABS systems. These systems, consisting of a ParA ATPase, a DNA binding ParB CTPase, and centromere sites parS, orchestrate the separation of newly replicated DNA copies and their intracellular positioning. Accurate segregation relies on the assembly of a high-molecular-weight complex, comprising a few hundreds of ParB dimers nucleated from parS sites. This complex assembles in a multi-step process and exhibits dynamic liquid-droplet properties. Despite various proposed models, the complete mechanism for partition complex assembly remains elusive. This study investigates the impact of DNA supercoiling on ParB DNA binding profiles in vivo, using the ParABS system of the plasmid F. We found that variations in DNA supercoiling does not significantly affect any steps in the assembly of the partition complex. Furthermore, physical modeling, leveraging ChIP-seq data from linear plasmids F, suggests that ParB sliding is restricted to approximately 2-Kbp from parS, highlighting the necessity for additional mechanisms beyond ParB sliding over DNA for concentrating ParB into condensates nucleated at parS. Lastly, explicit simulations of a polymer coated with bound ParB suggest a dominant role for ParB-ParB interactions in DNA compaction within ParB condensates.

Despite 15 years of extensive investigation, the fabrication and study of nanofluidic devices that incorporate a single carbon nanotube (CNT) still represents a remarkable experimental challenge. In this study, we present the fabrication of nanofluidic devices that integrate an individual single-walled CNT (SWCNT), showcasing a notable reduction in noise by 1 -3 orders of magnitude compared to conventional devices. This achievement was made possible by employing high dielectric constant materials for both the substrate and the CNT-covering layer. Furthermore, we provide a detailed account of the crucial factors contributing to the successful fabrication of SWCNT-based nanofluidic devices that are reliably leak-free, plug-free, and long-lived. Key considerations include the quality of the substrate-layer interface, the nanotube opening, and the effective removal of photoresist residues and trapped microbubbles. We demonstrate that these devices, characterized by a high signal-tonoise ratio, enable spectral noise analysis of ionic transport through an individual SWCNT, thus showing that SWCNTs obey Hooge's law in 1/ f at low frequencies. Beyond advancing our fundamental understanding of ion transport in SWCNTs, these ultralow-noise measurements open avenues for leveraging SWCNTs in nanopore sensing applications for single-molecule detection, offering high sensitivity and identification capabilities.

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.