Diffusion and subdiffusion of interacting particles on comb-like structures

We study the dynamics of a tracer particle (TP) on a comb lattice populated by randomly moving hard-core particles in the dense limit. We first consider the case where the TP is constrained to move on the backbone of the comb only, and, in the limit of high density of particles, we present exact analytical results for the cumulants of the TP position, showing a subdiffusive behavior $\sim t^{3/4}$. At longer times, a second regime is observed, where standard diffusion is recovered, with a surprising non analytical dependence of the diffusion coefficient on the particle density. When the TP is allowed to visit the teeth of the comb, based on a mean-field-like Continuous Time Random Walk description, we unveil a rich and complex scenario, with several successive subdiffusive regimes, resulting from the coupling between the inhomogeneous comb geometry and particle interactions. Remarkably, the presence of hard-core interactions speeds up the TP motion along the backbone of the structure in all regimes.Comment: 5 pages, 3 figures + supplemental materia

Microscopic theory for negative differential mobility in crowded environments

We study the behavior of the stationary velocity of a driven particle in an environment of mobile hard-core obstacles. Based on a lattice gas model, we demonstrate analytically that the drift velocity can exhibit a nonmonotonic dependence on the applied force, and show quantitatively that such negative differential mobility (NDM), observed in various physical contexts, is controlled by both the density and diffusion time scale of obstacles. Our study unifies recent numerical and analytical results obtained in specific regimes, and makes it possible to determine analytically the region of the full parameter space where NDM occurs. These results suggest that NDM could be a generic feature of biased (or active) transport in crowded environments.Comment: 5 pages, 2 figures + supplemental materia

Experimental observation of flow fields around active Janus spheres

The phoretic mechanisms at stake in the propulsion of asymmetric colloids have been the subject of debates during the past years. In particular, the importance of electrokinetic effects on the motility of Pt-PS Janus sphere was recently discussed. Here, we probe the hydrodynamic flow field around a catalytically active colloid using particle tracking velocimetry both in the freely swimming state and when kept stationary with an external force. Our measurements provide information about the fluid velocity in the vicinity of the surface of the colloid, and confirm a mechanism for propulsion that was proposed recently. In addition to offering a unified understanding of the nonequilibrium interfacial transport processes at stake, our results open the way to a thorough description of the hydrodynamic interactions between such active particles and understanding their collective dynamics

Distinct Behaviour of the Homeodomain Derived Cell Penetrating Peptide Penetratin in Interaction with Different Phospholipids

Penetratin is a protein transduction domain derived from the homeoprotein Antennapedia. Thereby it is currently used as a cell penetrating peptide to introduce diverse molecules into eukaryotic cells, and it could also be involved in the cellular export of transcription factors. Moreover, it has been shown that it is able to act as an antimicrobial agent. The mechanisms involved in all these processes are quite controversial.In this article, we report spectroscopic, calorimetric and biochemical data on the penetratin interaction with three different phospholipids: phosphatidylcholine (PC) and phosphatidylethanolamine (PE) to mimic respectively the outer and the inner leaflets of the eukaryotic plasma membrane and phosphatidylglycerol (PG) to mimic the bacterial membrane. We demonstrate that with PC, penetratin is able to form vesicle aggregates with no major change in membrane fluidity and presents no well defined secondary structure organization. With PE, penetratin aggregates vesicles, increases membrane rigidity and acquires an α-helical structure. With PG membranes, penetratin does not aggregate vesicles but decreases membrane fluidity and acquires a structure with both α-helical and β–sheet contributions.These data from membrane models suggest that the different penetratin actions in eukaryotic cells (membrane translocation during export and import) and on prokaryotes may result from different peptide and lipid structural arrangements. The data suggest that, for eukaryotic cell penetration, penetratin does not acquire classical secondary structure but requires a different conformation compared to that in solution

Harmonization and standardization of nucleus pulposus cell extraction and culture methods

Background In vitro studies using nucleus pulposus (NP) cells are commonly used to investigate disc cell biology and pathogenesis, or to aid in the development of new therapies. However, lab-to-lab variability jeopardizes the much-needed progress in the field. Here, an international group of spine scientists collaborated to standardize extraction and expansion techniques for NP cells to reduce variability, improve comparability between labs and improve utilization of funding and resources. Methods The most commonly applied methods for NP cell extraction, expansion, and re-differentiation were identified using a questionnaire to research groups worldwide. NP cell extraction methods from rat, rabbit, pig, dog, cow, and human NP tissue were experimentally assessed. Expansion and re-differentiation media and techniques were also investigated. Results Recommended protocols are provided for extraction, expansion, and re-differentiation of NP cells from common species utilized for NP cell culture. Conclusions This international, multilab and multispecies study identified cell extraction methods for greater cell yield and fewer gene expression changes by applying species-specific pronase usage, 60–100 U/ml collagenase for shorter durations. Recommendations for NP cell expansion, passage number, and many factors driving successful cell culture in different species are also addressed to support harmonization, rigor, and cross-lab comparisons on NP cells worldwide

'Fuelled' motion: Phoretic motility and collective behaviour of active colloids

Designing microscopic and nanoscopic self-propelled particles and characterising their motion have become a major scientific challenge over the past few decades. To this purpose, phoretic effects, namely propulsion mechanisms relying on local field gradients, have been the focus of many theoretical and experimental studies. In this review, we adopt a tutorial approach to present the basic physical mechanisms at stake in phoretic motion, and describe the different experimental works that led to the fabrication of active particles based on this principle. We also present the collective effects observed in assemblies of interacting active colloids, and the theoretical tools that have been used to describe phoretic and hydrodynamic interactions. © The Royal Society of Chemistry 2017

Comment on “Relative Diffusivities of Bound and Unbound Protein Can Control Chemotactic Directionality”

This is a comment on a recently published paper in Langmuir: Mandal, N. S.; Sen, A. Relative Diffusivities of Bound and Unbound Protein Can Control Chemotactic Directionality. Langmuir 2021, PMID: 34647749 [arXiv:2103.13469]. In this study, Mandal and Sen claim to propose a new kinetic model to analyze the directional movement of enzyme molecules in response to a gradient of their substrate, with the supposedly new prediction that net movement occurs up the substrate gradient when the diffusivity of the substrate-bound enzyme is lower than that of the unbound enzyme, and movement down the substrate gradient when the diffusivity of the substrate-bound enzyme is higher than that of the unbound enzyme. They develop this theoretical scheme to present an alternative to our previously published theoretical framework [Agudo-Canalejo, J.; Illien, P.; Golestanian, R. Phoresis and enhanced diffusion compete in enzyme chemotaxis. Nano Lett. 2018, 18, 2711-2717; arXiv:2104.02394]. We demonstrate that despite their claim, what they present is exactly the same theory as our work, and therefore, we conclude that their claim of novelty is unsubstantiated.Comment: This is a comment on arXiv:2103.13469 and concerns arXiv:2104.0239

Diffusion of an enzyme: the role of fluctuation-induced hydrodynamic coupling

The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is shown that equilibrium fluctuations can lead to an interplay between the internal and the external degrees of freedom and give rise to negative contributions to the overall diffusion coefficient. Considering that this model enzyme explores a mechanochemical cycle, we show how substrate binding and unbinding affects its internal fluctuations, and how this can result in an enhancement of the overall diffusion coefficient of the molecule. These theoretical predictions are successfully confronted with recent measurements of enzyme diffusion in dilute conditions using fluorescence correlation spectroscopy