Rotational and translational drags of a Janus particle close to a wall and a lipid membrane.

Hypothesis: Measuring rotational and translational Brownian motion of single spherical particles reveals dissipations due to the interaction between the particle and the environment.

Experiments: In this article, we show experiments where the in-plane translational and the two rotational drag coefficients of a single spherical Brownian particle can be measured. These particle drags are functions of the particle size and of the particle-wall distance, and of the viscous dissipations at play.

Stress overshoot, hysteresis, and the Bauschinger effect in sheared dense colloidal suspensions.

The mechanical nonlinear response of dense Brownian suspensions of polymer gel particles is studied experimentally and by means of numerical simulations. It is shown that the response to the application of a constant shear rate depends on the previous history of the suspension. When the flow starts from a suspension at rest, it exhibits an elastic response followed by a stress overshoot and then a plastic flow regime.

Coarse-grained description of monounsaturated peroxidized phospholipid bilayers.

Lipid peroxides result from a reaction between cis-unsaturated lipid chains and singlet oxygen molecules leading to the addition of a peroxide OOH side group next to the acyl-chain double bond. It is now established that HP-POPC (hydroperoxidized POPC) molecules form stable, thin, and laterally expanded bilayers. The difference in the structural organization arises from the hydrophilic character of the OOH side group that has a strong affinity with the water interface region, leading to significant reorganization of the bilayer.

Perturbing the catenoid: Stability and mechanical properties of nonaxisymmetric minimal surfaces.

Minimal surface problems arise naturally in many soft matter systems whose free energies are dominated by surface or interface energies. Of particular interest are the shapes, stability, and mechanical stresses of minimal surfaces spanning specific geometric boundaries. The "catenoid" is the best-known example where an analytical solution is known which describes the form and stability of a minimal surface held between two parallel, concentric circular frames.

Rheology of sliding leaflets in coarse-grained DSPC lipid bilayers.

Amphiphilic lipid bilayers modify the friction properties of the surfaces on top of which they are deposited. In particular, the measured sliding friction coefficient can be significantly reduced compared with the native surface. We investigate in this work the friction properties of a numerical coarse-grained model of DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine) lipid bilayer subject to longitudinal shear.

Ripple-like instability in the simulated gel phase of finite size phosphocholine bilayers.

Atomistic molecular dynamics simulations have reached a degree of maturity that makes it possible to investigate the lipid polymorphism of model bilayers over a wide range of temperatures. However if both the fluid L and tilted gel [Formula: see text] states are routinely obtained, the [Formula: see text] ripple phase of phosphatidylcholine lipid bilayers is still unsatifactorily described. Performing simulations of lipid bilayers made of different numbers of DPPC (1,2-dipalmitoylphosphatidylcholine) molecules ranging from 32 to 512, we demonstrate that the tilted gel phase [Formula: see text] expected below the pretransition cannot be obtained for large systems (equal or larger than 94 DPPC molecules) through common simulations settings or temperature treatments.

Molecular organization in hydroperoxidized POPC bilayers.

Lipid hydroperoxides are the primary reaction products of lipid oxidation, a natural outcome of life under oxygen. While playing a major role in cell metabolism, the microscopic origins of the effects of lipid hydroperoxidation on biomembranes remain elusive. Here we probe the polar structure of partially to fully hydroperoxidized bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) by a combination of environment-sensitive fluorescent probes and coarse-grained Martini numerical simulations.

MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes.

Machine Learning-assisted Lipid Phase Analysis (MLLPA) is a new Python 3 module developed to analyze phase domains in a lipid membrane based on lipid molecular states. Reading standard simulation coordinate and trajectory files, the software first analyze the phase composition of the lipid membrane by using machine learning tools to label each individual molecules with respect to their state, and then decompose the simulation box using Voronoi tessellations to analyze the local environment of all the molecules of interest. MLLPA is versatile as it can read from multiple format (e.

Accumulation of styrene oligomers alters lipid membrane phase order and miscibility.

Growth of plastic waste in the natural environment, and in particular in the oceans, has raised the accumulation of polystyrene and other polymeric species in eukyarotic cells to the level of a credible and systemic threat. Oligomers, the smallest products of polymer degradation or incomplete polymerization reactions, are the first species to leach out of macroscopic or nanoscopic plastic materials. However, the fundamental mechanisms of interaction between oligomers and polymers with the different cell components are yet to be elucidated.

A machine learning study of the two states model for lipid bilayer phase transitions.

We have adapted a set of classification algorithms, also known as machine learning, to the identification of fluid and gel domains close to the main transition of dipalmitoyl-phosphatidylcholine (DPPC) bilayers. Using atomistic molecular dynamics conformations in the low and high temperature phases as learning sets, the algorithm was trained to categorise individual lipid configurations as fluid or gel, in relation with the usual two-states phenomenological description of the lipid melting transition. We demonstrate that our machine can learn and sort lipids according to their most likely state without prior assumption regarding the nature of the order parameter of the transition.

Coarse-Grain Simulations of Solid Supported Lipid Bilayers with Varying Hydration Levels.

Supported lipid bilayers (SLBs) are a very popular system for the study of biomimetic membranes. Understanding of the interactions between the solid substrate and the lipid membrane opens pathways to the design of new materials with fine-tunable properties. While it is possible to study SLBs via molecular dynamics (MD) simulations, difficulties still remain for these strategies; in particular, the confined water layer thickness and structure are difficult to reproduce in simulations.

Interaction of Giant Unilamellar Vesicles with the Surface Nanostructures on Dragonfly Wings.

The waxy epicuticle of dragonfly wings contains a unique nanostructured pattern that exhibits bactericidal properties. In light of emerging concerns of antibiotic resistance, these mechano-bactericidal surfaces represent a particularly novel solution by which bacterial colonization and the formation of biofilms on biomedical devices can be prevented. Pathogenic bacterial biofilms on medical implant surfaces cause a significant number of human deaths every year.

Kinetic evolution of DOPC lipid bilayers exposed to α-cyclodextrins.

Cyclodextrins are cyclic oligosaccharides capable of forming inclusion complexes with a variety of molecules, and as such have been recognized as a pharmaceutical and biotechnological asset. Cyclodextrins are known to interact with the components of cell membranes, and this correlates with a significant degree of cytotoxicity. In this work, we report on the mechanism of degradation of a model dioleoyl-phosphatidylcholine (DOPC) bilayer exposed to a solution with increasing concentrations of α-cyclodextrins.

Permeability of DOPC bilayers under photoinduced oxidation: Sensitivity to photosensitizer.

The modification of lipid bilayer permeability is one of the most striking yet poorly understood physical transformations that follow photoinduced lipid oxidation. We have recently proposed that the increase of permeability of photooxidized 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers is controlled by the time required by the oxidized lipid species to diffuse and aggregate into pores. Here we further probe this mechanism by studying photosensitization of DOPC membranes by methylene blue (MB) and DO15, a more hydrophobic phenothiazinium photosensitizer, under different irradiation powers.

DPPC Bilayers in Solutions of High Sucrose Content.

The properties of lipid bilayers in sucrose solutions have been intensely scrutinized over recent decades because of the importance of sugars in the field of biopreservation. However, a consensus has not yet been formed on the mechanisms of sugar-lipid interaction. Here, we present a study on the effect of sucrose on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayers that combines calorimetry, spectral fluorimetry, and optical microscopy.

Influence of a pH-sensitive polymer on the structure of monoolein cubosomes.

Cubosomes consist in submicron size particles of lipid bicontinuous cubic phases stabilized by surfactant polymers. They provide an appealing road towards the practical use of lipid cubic phases for pharmaceutical and cosmetic applications, and efforts are currently being made to control the encapsulation and release properties of these colloidal objects. We overcome in this work the lack of sensitivity of monoolein cubosomes to pH conditions by using a pH sensitive polymer designed to strongly interact with the lipid structure at low pH.

Hemodynamic forces can be accurately measured in vivo with optical tweezers.

Force sensing and generation at the tissue and cellular scale is central to many biological events. There is a growing interest in modern cell biology for methods enabling force measurements in vivo. Optical trapping allows noninvasive probing of piconewton forces and thus emerged as a promising mean for assessing biomechanics in vivo.

Peroxidised phospholipid bilayers: insight from coarse-grained molecular dynamics simulations.

An original coarse-grained model for peroxidised phospholipids is presented, based on the MARTINI lipid force field. This model results from a combination of thermodynamic modelling and structural information on the area per lipid, which have been made available recently. The resulting coarse-grained lipid molecules form stable bilayers, and a set of elastic coefficients (compressibility and bending moduli) is obtained.

Physical damage on giant vesicles membrane as a result of methylene blue photoirradiation.

In this study we pursue a closer analysis of the photodamage promoted on giant unilamellar vesicles membranes made of dioleoyl-sn-glycero-3-phosphocholine (DOPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), by irradiating methylene blue present in the giant unilamellar vesicles solution. By means of optical microscopy and electro-deformation experiments, the physical damage on the vesicle membrane was followed and the phospholipids oxidation was evaluated in terms of changes in the membrane surface area and permeability. As expected, oxidation modifies structural characteristics of the phospholipids that lead to remarkable membrane alterations.

Scraping and stapling of end-grafted DNA chains by a bioadhesive spreading vesicle to reveal chain internal friction and topological complexity.

Stained end-grafted DNA molecules about 20 μm long are scraped away and stretched out by the spreading front of a bioadhesive vesicle. Tethered biotin ligands bind the vesicle bilayer to a streptavidin substrate, stapling the DNAs into frozen confinement paths. Image analysis of the stapled DNA gives access, within optical resolution, to the local stretching values of individual DNA molecules swept by the spreading front, and provides evidence of self-entanglements.

Surfactant distribution in waterborne acrylic films. 1. Bulk investigation.

The distribution of an anionic surfactant, sodium dodecyl sulfate (SDS), in waterborne acrylic films was investigated, focusing on the effects of particle composition and size, and pH of the latex. The observed surfactant distributions could be classified in two categories: homogeneous and heterogeneous, the latter showing SDS aggregates. The shape of the profiles was related to the stability of the latex during drying, at short interparticular distances.

Fast algorithms for classical X-->0 diffusion-reaction processes.

The Doi formalism treats a reaction-diffusion process as a quantum many-body problem. We use this second-quantized formulation as a starting point to derive a numerical scheme for simulating X-->0 reaction-diffusion processes, following a well-established time discretization procedure. In the case of a reaction zone localized in the configuration space, this formulation provides also a systematic way of designing an optimized, multiple time step algorithm, spending most of the computation time to sample the configurations where the reaction is likely to occur.

Ligand-receptor interactions in chains of colloids: when reactions are limited by rotational diffusion.

We discuss the theory of ligand receptor reactions between two freely rotating colloids in close proximity to one other. Such reactions, limited by rotational diffusion, arise in magnetic bead suspensions where the beads are driven into close contact by an applied magnetic field as they align in chainlike structures. By a combination of reaction-diffusion theory, numerical simulations, and heuristic arguments, we compute the time required for a reaction to occur in a number of experimentally relevant situations.

Trotter derivation of algorithms for Brownian and dissipative particle dynamics.

This paper focuses on the temporal discretization of the Langevin dynamics, and on different resulting numerical integration schemes. Using a method based on the exponentiation of time dependent operators, we carefully derive a numerical scheme for the Langevin dynamics, which we found equivalent to the proposal of Ermak and Buckholtz [J. Comput.

Collision induced spatial organization of microtubules.

The dynamic behavior of microtubules in solution can be strongly modified by interactions with walls or other structures. We examine here a microtubule growth model where the increase in size of the plus-end is perturbed by collisions with other microtubules. We show that such a simple mechanism of constrained growth can induce ordered structures and patterns from an initially isotropic and homogeneous suspension.