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Apollonian packing in polydisperse emulsions
Laboratoire Colloïdes et Matériaux Divisés - Sylvie Kwok, Robert Botet, Lewis Sharpnack and Bernard Cabane
Nature Protocols - 16 2426-2430 - https://doi.org/10.1039/C9SM01772K - 2020
We have discovered the existence of polydisperse high internal-phase-ratio emulsions (HIPE) in which the internal-phase droplets, present at 95% volume fraction, remain spherical and organise themselves according to Apollonian packing rules. These polydisperse HIPEs are formed by emulsifying oil dropwise in a surfactant-poor aqueous continuous phase. After stirring has ceased, their droplet size distributions begin to evolve spontaneously and continuously through coalescence towards well-defined power laws with the Apollonian exponent. Small-angle X-ray Scattering performed on aged HIPEs demonstrate that the droplet packing structure agrees with that of a numerically simulated random Apollonian packing. We argue that when such concentrated emulsions are allowed to evolve, the coalescing droplets must obey volume and sphericity conservation. This leads to a mechanism that differs from typical coalescence in dilute emulsions.

Swelling, dewetting and breakup in thin polymer films for cultural heritage
Laboratoire Colloïdes et Matériaux Divisés - Amélie Castel, Philipp Gutfreund, Bernard Cabaned and Yahya Rharbi
Soft Matter - 16 1485-1497 - https://doi.org/10.1039/C9SM01976F - 2020
The removal of ultrathin amorphous polymer films in contact with nonsolvent/solvent binary mixtures is addressed by means of neutron reflectometry and atomic force microscopy. The high resolution of neutron scattering makes it possible to resolve the distribution profiles of heavy water and benzyl alcohol inside Laropal®A81, often employed as a protective varnish layer for Culture Heritage in restoration of easel paintings. The swelling kinetics and distribution profiles were recorded as a function of time and increasing benzyl alcohol concentration in water. The varnish film swells by penetration of the good solvent. At higher concentrations water-filled cavities appear inside the varnish and grow with time. Contrary to homogeneous dissolution dewetting is observed at late stages of exposure to the liquid which leads to the Breakup of the film. The high resolution measurements are compared to bulk behaviour characterized by the ternary phase diagram and the Flory–Huggins interaction parameters are calculated and used to predict the swelling and solvent partition in the films. Distinct differences of the thin film to bulk behaviour are found. The expectations made previously for the behaviour of solvent/non-solvent mixtures on the removal of thin layers in the restoration of easel paintings should be revised in view of surface interactions.

Optimised hyperbolic microchannels for the mechanical characterisation of bio-particles
Laboratoire Complex Suspensions - Yanan Liu, Konstantinos Zografos, Joana Fidalgo, Charles Duchene, Clement Quintard, Thierry Darnige, Vasco Filipe, Sylvain Huille, Olivia du Roure, Monica S. N. Oliveira and Anke Lindner
Soft Matter - 16 9844 - DOI: 10.1039/d0sm01293a - 2020
The transport of bio-particles in viscous flows exhibits a rich variety of dynamical behaviour, such as
morphological transitions, complex orientation dynamics or deformations. Characterising such complex
behaviour under well controlled flows is key to understanding the microscopic mechanical properties of
biological particles as well as the rheological properties of their suspensions. While generating regions of
simple shear flow in microfluidic devices is relatively straightforward, generating straining flows in which
the strain rate is maintained constant for a sufficiently long time to observe the objects’ morphologic
evolution is far from trivial. In this work, we propose an innovative approach based on optimised design
of microfluidic converging–diverging channels coupled with a microscope-based tracking method to
characterise the dynamic behaviour of individual bio-particles under homogeneous straining flow.
The tracking algorithm, combining a motorised stage and a microscopy imaging system controlled by
external signals, allows us to follow individual bio-particles transported over long-distances with highquality
images. We demonstrate experimentally the ability of the numerically optimised microchannels
to provide linear velocity streamwise gradients along the centreline of the device, allowing for extended
consecutive regions of homogeneous elongation and compression. We selected three test cases (DNA,
actin filaments and protein aggregates) to highlight the ability of our approach for investigating dynamics
of objects with a wide range of sizes, characteristics and behaviours of relevance in the biological world
Meta population structure and the evolutionary transition to multicellularity
Laboratoire de Génétique de l’Evolution - Caroline J. Rose Katrin Hammerschmidt Yuriy Pichugin Paul B. Rainey
First published - 23(9) 1380-1390 - doi.org/10.1111/ele.13570 - 2020
The evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. Here, using experimental bacterial populations as proxies for nascent multicellular organisms, we manipulate ecological factors shaping the evolution of groups. Groups were propagated under regimes requiring reproduction via a life cycle replete with developmental and dispersal (propagule) phases, but in one treatment lineages never mixed, whereas in a second treatment, cells from different lineages experienced intense competition during the dispersal phase. The latter treatment favoured traits promoting cell growth at the expense of traits underlying group fitness – a finding that is supported by results from a mathematical model. Our results show that the transition to multicellularity benefits from ecological conditions that maintain discreteness not just of the group (soma) phase, but also of the dispersal (germline) phase.

Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet‐associated Pseudomonas in Oxford and Auckland
Laboratoire de Génétique de l’Evolution - Xue‐Xian Zhang,corresponding author, Stephen R. Ritchie, Hao Chang, Dawn L. Arnold, Robert W. Jackson, and Paul B. Rainey
Ecol Evol - 10(12) 5963–5975 - doi: 10.1002/ece3.6334 - 2020
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.

Laboratoire de Génétique de l’Evolution - Paul RAINEY Jérôme BIBETTE Jean BAUDRY Nicolas BREMOND Laurent BOITARD Jairo GARNICA Denis COTTINET
My Science Work - - - 2020
The present invention relates to a method for manipulating the evolution of collectives of self-replicating entities and/or variation between collectives of self-replicating entities, in a high throughput droplet milli-fluidic system.
Experimental manipulation of selfish genetic elements links genes to microbial community function
Laboratoire de Génétique de l’Evolution - Steven D. Quistad, Guilhem Doulcier and Paul B. Rainey
Philosophical Transactions of the Royal Society - - doi.org/10.1098/rstb.2019.0681 - 2020
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function.

Toward a dynamical understanding of microbial communities
Laboratoire de Génétique de l’Evolution - Paul B. Rainey and Steven D. Quistad
Philosophical Transactions of the Royal Society - - doi.org/10.1098/rstb.2019.0248 - 2020
The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry.

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity
Laboratoire de Génétique de l’Evolution - Guilhem Doulcier, Amaury Lambert, Silvia De Monte, Paul B Rainey
EcologyEvolutionary Biology - - DOI: 10.7554/eLife.53433 - 2020
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.

Ecological scaffolding and the evolution of individuality
Laboratoire de Génétique de l’Evolution - Andrew J. Black, Pierrick Bourrat & Paul B. Rainey
Nature Ecology & Evolution - 4 426–436 - doi.org/10.1038/s41559-019-1086-9 - 2020
Evolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here, we emphasize this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions. Using mechanistic mathematical models, we show how a minimal ecological structure comprising patchily distributed resources and between-patch dispersal can scaffold Darwinian-like properties on collectives of cells. This scaffolding causes cells to participate directly in the process of evolution by natural selection as if they were members of multicellular collectives, with collectives participating in a death–birth process arising from the interplay between the timing of dispersal events and the rate of resource use by cells. When this timescale is sufficiently long and new collectives are founded by single cells, collectives experience conditions that favour evolution of a reproductive division of labour. Together our simple model makes explicit key events in the major evolutionary transition to multicellularity. It also makes predictions concerning the life history of certain pathogens and serves as an ecological recipe for experimental realization of evolutionary transitions.

Near-surface rheology and hydrodynamic boundary condition of semi-dilute polymer solutions
Laboratoire Indysoft - Gabriel Guyard Alexandre Vilquin Nicolas Sanson Frederic Restagno Joshua D. Mcgraw
HAL - 1 - https://hal.archives-ouvertes.fr/hal-03029154 - 2020
Understanding confined flows of complex fluids requires simultaneous access to the mechanical behaviour of the liquid and the boundary condition at the interfaces. Here, we use evanescent wave microscopy to investigate near-surface flows of semi-dilute, unentangled polyacrylamide solutions. By using both neutral and anionic polymers, we show that monomer charge plays a key role in confined polymer dynamics. For solutions in contact with glass, the neutral polymers display chain-sized adsorbed layers, while a shear-rate-dependent apparent slip length is observed for anionic polymer solutions. The slip lengths measured at all concentrations collapse onto a master curve when scaled using a simple two-layer depletion model with non-Newtonian viscosity. A transition from an apparent slip boundary condition to a chain-sized adsorption layer is moreover highlighted by screening the charge with additional salt in the anionic polymer solutions. We anticipate that our study will be a starting point for more complex studies relating the polymer dynamics at interfaces to their chemical and physical composition.
Interface-Sensitive Raman Microspectroscopy of Water via Confinement with a Multimodal Miniature Surface Forces Apparatus
Laboratoire INDYSOFT - Hilton B. de Aguiar, Joshua D. McGraw, and Stephen H. Donaldson Jr.
Langmuir - 35(48) 15543–15551 - doi.org/10.1021/acs.langmuir.9b01889 - 2020
Modern interfacial science is increasingly multidisciplinary. Unique insight into interfacial interactions requires new multimodal techniques for interrogating surfaces with simultaneous complementary physical and chemical measurements. Here, we describe the design and testing of a microscope that incorporates a miniature surface forces apparatus (μSFA) in sphere vs flat geometry for force–distance measurements, while simultaneously acquiring Raman spectra of the confined zone. The simple optical setup isolates independent optical paths for (i) the illumination and imaging of Newton’s rings and (ii) Raman scattering excitation and efficient signal collection. We benchmark the methodology by examining Teflon thin films in asymmetric (Teflon–water–glass) and symmetric (Teflon–water–Teflon) configurations. Water is observed near the Teflon–glass interface with nanometer-scale sensitivity in both the distance and Raman signals. We perform chemically resolved, label-free imaging of confined contact regions between Teflon and glass surfaces immersed in water. Remarkably, we estimate that the combined approach enables vibrational spectroscopy with single water monolayer sensitivity within minutes. Altogether, the Raman-μSFA allows exploration of molecular confinement between surfaces with chemical selectivity and correlation with interaction forces.
Multimodal Miniature Surface Forces Apparatus (μSFA) for Interfacial Science Measurements
Laboratoire INDYSOFT - Kai Kristiansen, Stephen H. Donaldson Jr., Zachariah J. Berkson, Jeffrey Scott, Rongxin Su, Xavier Banquy, Dong Woog Lee, Hilton B. de Aguiar, Joshua D. McGraw, George D. Degen, and Jacob N. Israelachvili
Langmuir - 35(48) 15500–15514 - doi.org/10.1021/acs.langmuir.9b01808 - 2020
Advances in the research of intermolecular and surface interactions result from the development of new and improved measurement techniques and combinations of existing techniques. Here, we present a new miniature version of the surface forces apparatus—the μSFA—that has been designed for ease of use and multimodal capabilities with the retention of the capabilities of other SFA models including accurate measurements of the surface separation distance and physical characterization of dynamic and static physical forces (i.e., normal, shear, and friction) and interactions (e.g., van der Waals, electrostatic, hydrophobic, steric, and biospecific). The small physical size of the μSFA, compared to previous SFA models, makes it portable and suitable for integration into commercially available optical and fluorescence light microscopes, as demonstrated here. The large optical path entry and exit ports make it ideal for concurrent force measurements and spectroscopy studies. Examples of the use of the μSFA in combination with surface plasmon resonance (SPR) and Raman spectroscopy measurements are presented. Because of the short working distance constraints associated with Raman spectroscopy, an interferometric technique was developed and applied to calculate the intersurface separation distance based on Newton’s rings. The introduction of the μSFA will mark a transition in SFA usage from primarily physical characterization to concurrent physical characterization with in situ chemical and biological characterization to study interfacial phenomena, including (but not limited to) molecular adsorption, fluid flow dynamics, the determination of surface species and morphology, and (bio)molecular binding kinetics.
Time dependence of advection-diffusion coupling for nanoparticle ensembles
Laboratoire INDYSOFT - Alexandre Vilquin Vincent Bertin Pierre Soulard Gabriel Guyard Elie Raphaël Frederic Restagno Thomas Salez Joshua Mcgraw
HAL - 1 - https://hal.archives-ouvertes.fr/hal-02896493 - 2020
Particle transport in fluids at micro-and nano-scales is important in many domains. As compared to the quiescent case, the time evolution of particle dispersion is enhanced by coupling: i) advection along the flow; and ii) diffusion along the associated velocity gradients. While there is a well-known, long-time limit for this advection-diffusion enhancement, understanding the short-time limit and corresponding crossover between these two asymptotic limits is less mature. We use evanescent-wave video microscopy for its spatio-temporal resolution. Specifically, we observe a near-surface zone of where the velocity gradients, and thus dispersion, are the largest within a simple microfluidic channel. Supported by a theoretical model and simulations based on overdamped Langevin dynamics, our experiments reveal the crossover of this so-called Taylor dispersion from short to long time scales. Studying a range of particle size, viscosity and applied pressure, we show that the initial spatial distribution of particles can strongly modify observed master curves for short-time dispersion and its crossover into the long-time regime.
Influence of outer-layer finite-size effects on the dewetting dynamics of a thin polymer film embedded in an immiscible matrix
Laboratoire INDYSOFT - M. S. Chebil,a J. D. McGraw, T. Salez, C. Sollogoub and G. Miquelard-Garnier
Soft Matter - 14 6256-6263 - doi.org/10.1039/C8SM00592C - 2020
In capillary-driven fluid dynamics, simple departures from equilibrium offer the chance to quantitatively model the resulting relaxations. These dynamics in turn provide insight on both practical and fundamental aspects of thin-film hydrodynamics. In this work, we describe a model trilayer dewetting experiment elucidating the effect of solid, no-slip confining boundaries on the bursting of a liquid film in a viscous environment. This experiment was inspired by an industrial polymer processing technique, multilayer coextrusion, in which thousands of alternating layers are stacked atop one another. When pushed to the nanoscale limit, the individual layers are found to break up on time scales shorter than the processing time. To gain insight on this dynamic problem, we here directly observe the growth rate of holes in the middle layer of the trilayer films described above, wherein the distance between the inner film and solid boundary can be orders of magnitude larger than its thickness. Under otherwise identical experimental conditions, thinner films break up faster than thicker ones. This observation is found to agree with a scaling model that balances capillary driving power and viscous dissipation with a no-slip boundary condition at the solid substrate/viscous environment boundary. In particular, even for the thinnest middle-layers, no finite-size effect related to the middle film is needed to explain the data. The dynamics of hole growth is captured by a single master curve over four orders of magnitude in the dimensionless hole radius and time, and is found to agree well with predictions including analytical expressions for the dissipation.
Adsorption-induced slip inhibition for polymer melts on ideal substrates
Laboratoire INDYSOFT - Mark Ilton, Thomas Salez, Paul D. Fowler, Marco Rivetti, Mohammed Aly, Michael Benzaquen, Joshua D. McGraw, Elie Raphaël, Kari Dalnoki-Veress & Oliver Bäumchen
Nat Commun - 9 1172 - doi.org/10.1039/C8SM00592C - 2020
Hydrodynamic slip, the motion of a liquid along a solid surface, represents a fundamental phenomenon in fluid dynamics that governs liquid transport at small scales. For polymeric liquids, de Gennes predicted that the Navier boundary condition together with polymer reptation implies extraordinarily large interfacial slip for entangled polymer melts on ideal surfaces; this Navier-de Gennes model was confirmed using dewetting experiments on ultra-smooth, low-energy substrates. Here, we use capillary leveling—surface tension driven flow of films with initially non-uniform thickness—of polymeric films on these same substrates. Measurement of the slip length from a robust one parameter fit to a lubrication model is achieved. We show that at the low shear rates involved in leveling experiments as compared to dewetting ones, the employed substrates can no longer be considered ideal. The data is instead consistent with a model that includes physical adsorption of polymer chains at the solid/liquid interface.
Self-Similar Relaxation of Confined Microfluidic Droplets
Laboratoire INDYSOFT - Margaux Kerdraon1, Joshua D. McGraw1, Benjamin Dollet2, and Marie-Caroline Jullien
Phys. Rev. Lett. - 123 024501 - doi.org/10.1103/PhysRevLett.123.024501 - 2020
We report an experimental study concerning the capillary relaxation of a confined liquid droplet in a microscopic channel with a rectangular cross section. The confinement leads to a droplet that is extended along the direction normal to the cross section. These droplets, found in numerous microfluidic applications, are pinched into a peanutlike shape thanks to a localized, reversible deformation of the channel. Once the channel deformation is released, the droplet relaxes back to a pluglike shape. During this relaxation, the liquid contained in the central pocket drains towards the extremities of the droplet. Modeling such viscocapillary droplet relaxation requires considering the problem as 3D due to confinement. This 3D consideration yields a scaling model incorporating dominant dissipation within the droplet menisci. As such, the self-similar droplet dynamics is fully captured.
Natural Abundance Oxygen-17 Solid-State NMR of Metal Organic Frameworks Enhanced by Dynamic Nuclear Polarization
Laboratoire Institut des Matériaux Poreux de Paris - Carnevale D, Mouchaham G, Wang S, Baudin M, Serre C, Bodenhausen G, Abergel D
ChemRxiv - - DOI: 10.26434/chemrxiv.12477449.v1 - 2020
The 17O resonances of Zirconium-oxo clusters that can be found in porous Zr carboxylate metal-organic frameworks (MOFs) have been investigated by magic-angle spinning (MAS) NMR spectroscopy enhanced by dynamic nuclear polarization (DNP). High-resolution 17O spectra at 0.037 % natural abundance could be obtained in 48 hours, thanks to DNP enhancement of the 1H polarization by factors e(1H) = Swith/Swithout = 28, followed by 1H®17O cross-polarization, allowing a saving in experimental time by a factor of ca. 800. The distinct 17O sites from the oxo-clusters can be resolved at 18.8 T. Their assignment is supported by density functional theory (DFT) calculations of chemical shifts and quadrupolar parameters.
One‐step versatile room temperature synthesis of metal(IV) carboxylate MOFs
Laboratoire Institut des Matériaux Poreux de Paris - Shan Dai, Farid Nouar, Sanjun Zhang, Antoine Tissot, and Christian Serre
Angew. Chem. Int. Ed - - : https://doi.org/10.1002/anie.202014184 - 2020
This manuscript has been accepted after peer review and appears as an Accepted Article online prior to editing, proofing, and formal publication of the final Version of Record (VoR). This work is currently citable by using the Digital Object Identifier (DOI) given below. The VoR will be published online in Early View as soon as possible and may be different to this Accepted Article as a result of editing. Readers should obtain
the VoR from the journal website shown below when it is published to ensure accuracy of information. The authors are responsible for the content of this Accepted Article.
Principal Component Analysis (PCA) for Powder Diffraction Data: Towards Unblinded Applications
Laboratoire Institut des Matériaux Poreux de Paris - Shan Dai, Farid Nouar, Sanjun Zhang, Antoine Tissot, and Christian Serre
Angew. Chem. Int. Ed - - doi.org/10.1002/anie.202014184 - 2020
The development of room temperature green syntheses of robust MOFs is of great interest to meet the demand of the sustainable chemistry and is a pre‐requisite for the incorporation of functional but fragile compounds in water stable MOFs. However, only few ambient conditions routes to produce metal(IV) based MOFs have been reported and most of them suffer from a very low yield and/or multiple steps that preclude their use for most applications. We report here a new versatile one‐step synthesis of a series of highly porous M 6 oxoclusters based MOFs (M= Zr, Hf, Ce) at room temperature, including 8 or 12‐connected micro/mesoporous solids with different functionalized organic ligands. The resulting compounds show varying degrees of defectivity, particularly for 12‐connected phases, while maintaining the chemical stability of the parent MOFs. We propose first insights for the efficient MOF preparation based on In‐situ kinetics observations. Remarkably, the synthetic versatility not only allows an efficient room temperature synthesis with a high space‐time yield, but also gives possibility to tune the particle size, which therefore paves the way for their practical use.

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