Phase transitions in chromatin: Mesoscopic and mean-field approaches.

By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation within the fluid solvating chromatin, resulting in the formation of biocondensates; and (2) the coil-globule crossover of the chromatin fiber, which drives the condensation or extension of the chain. In our model, a species representing a domain of chromatin is embedded in a binary fluid. This fluid phase separates to form a droplet rich in a macromolecule (B).

Enhanced diffusion of tracer particles in nonreciprocal mixtures.

We study the diffusivity of a tagged particle in a binary mixture of Brownian particles with nonreciprocal interactions. Numerical simulations reveal that, for a broad class of interaction potentials, nonreciprocity can significantly increase the long-time diffusion coefficient of tracer particles and that this diffusion enhancement is associated with a breakdown of the Einstein relation. These observations are quantified and confirmed via two different and complementary analytical approaches: (i) a linearized stochastic density field theory, which is particularly accurate in the limit of soft interactions, and (ii) a reduced two-body description, which is exact at leading order in the density of particles.

Isotropic active colloids: explicit implicit descriptions of propulsion mechanisms.

Modeling the couplings between active particles often neglects the possible many-body effects that control the propulsion mechanism. Accounting for such effects requires the explicit modeling of the molecular details at the origin of activity. Here, we take advantage of a recent two-dimensional model of isotropic active particles whose propulsion originates from the interactions between solute particles in the bath.

Confined Electrolytes Show Bulk Dynamics Modulated by Hydrodynamic Couplings with the Walls.

We use numerical simulations at the mesoscopic scale, namely, multiparticle collision dynamics (MPCD), to investigate the properties of electrolyte solutions in a charged slit pore. The solution is described within the primitive model of electrolytes, where ions are charged hard spheres embedded in a dielectric medium. Hydrodynamic couplings between ions and with the charged walls are precisely accounted for by the MPCD algorithm.

Diffusion of a tracer in a dense mixture of soft particles connected to different thermostats.

We study the dynamics of a tracer in a dense mixture of particles connected to different thermostats. Starting from the overdamped Langevin equations that describe the evolution of the system, we derive the expression of the self-diffusion coefficient of a tagged particle in the suspension, in the limit of soft interactions between the particles. Our derivation, which relies on the linearization of the Dean-Kawasaki equations obeyed by the density fields and on a path-integral representation of the dynamics of the tracer, extends previous derivations that held for tracers in contact with a single bath.

Conditions for the propulsion of a colloid surrounded by a mesoscale phase separation.

We study a two-dimensional model of an active isotropic colloid whose propulsion is linked to the interactions between solute particles of the bath. The colloid catalyzes a chemical reaction in its vicinity, that yields a local phase separation of solute particles. The density fluctuations of solute particles result in the enhanced diffusion of the colloid.

Electroosmotic Flow Induced Lift Forces on Polymer Chains in Nanochannels.

A major objective of research in nanofluidics is to achieve better selectivity in manipulating the fluxes of nano-objects and in particular of biopolymers. Numerical simulations allow one to better understand the physical mechanisms at play in such situations. We performed hybrid mesoscale simulations to investigate the properties of polymers under flows in slit pores at the nanoscale.

Spontaneous propulsion of an isotropic colloid in a phase-separating environment.

The motion of active colloids is generally achieved through their anisotropy, as exemplified by Janus colloids. Recently, there was a growing interest in the propulsion of isotropic colloids, which requires some local symmetry breaking. Although several mechanisms for such propulsion were proposed, little is known about the role played by the interactions within the environment of the colloid, which can have a dramatic effect on its propulsion.

Coarse-Grained Models of Aqueous Solutions of Polyelectrolytes: Significance of Explicit Charges.

The structure of polyelectrolytes is highly sensitive to small changes in interactions between their monomers. In particular, interactions mediated by counterions play a significant role and are affected by both specific molecular effects and generic concentration effects. The ability of coarse-grained models to reproduce the structural properties of an atomic model is thus a challenging task.

Polymer coil-globule phase transition is a universal folding principle of Drosophila epigenetic domains.

Background: Localized functional domains within chromosomes, known as topologically associating domains (TADs), have been recently highlighted. In Drosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the "missing link" between epigenetics and gene activity. Recent observations (Boettiger et al.

Computation of the Hydrodynamic Radius of Charged Nanoparticles from Nonequilibrium Molecular Dynamics.

We have used nonequilibrium molecular dynamics to simulate the flow of water molecules around a charged nanoparticle described at the atomic scale. These nonequilibrium simulations allowed us to compute the friction coefficient of the nanoparticle and then to deduce its hydrodynamic radius. We have compared two different strategies to thermostat the simulation box, since the low symmetry of the flow field renders the control of temperature non trivial.

Comparison of different coupling schemes between counterions and charged nanoparticles in multiparticle collision dynamics.

We applied the multiparticle collision dynamics (MPC) simulation technique to highly asymmetric electrolytes in solution, i.e., charged nanoparticles and their counterions in a solvent.

Nonideal effects in electroacoustics of solutions of charged particles: combined experimental and theoretical analysis from simple electrolytes to small nanoparticles.

The electric signal induced by an ultrasonic wave in aqueous solutions of charged species is measured and analyzed. A device is developed which measures the raw induced electric signal for small sample volumes (few milliliters) and without any preceding calibration. The potential difference generated between two identical electrodes, called the ionic vibration potential (IVP), is thus easily deduced.

Critical effect of pore characteristics on capillary infiltration in mesoporous films.

Capillary phenomena governing the mass-transport (capillary filling, condensation/evaporation) has been experimentally investigated in around 20 different silica thin films exhibiting various porosities with pores dimension ranging from 2 to 200 nm. Films have been prepared by sol-gel chemistry combined with soft-templating approaches and controlled dip coating process. Environmental ellipsometric porosimetry combined with electronic microscopy were used to assess the porosity characteristics.

Dynamics of solutes with hydrodynamic interactions: comparison between Brownian dynamics and stochastic rotation dynamics simulations.

The dynamics of particles in solution or suspension is influenced by thermal fluctuations and hydrodynamic interactions. Several mesoscale methods exist to account for these solvent-induced effects such as Brownian dynamics with hydrodynamic interactions and hybrid molecular dynamics-stochastic rotation dynamics methods. Here we compare two ways of coupling solutes to the solvent with stochastic rotation dynamics (SRD) to Brownian dynamics with and without explicit hydrodynamic interactions.

Self-diffusion and activity coefficients of ions in charged disordered media.

Self-diffusion and single ion activity coefficients of ions of size symmetric electrolytes were studied in the presence of a collection of charged obstacles (called matrix) within a "soft" version of the primitive model of electrolyte solutions. The matrix subsystem possesses a net charge, depending on the concentration and charge of obstacles. The brownian dynamics method was used to calculate the self-diffusion coefficients of mobile species.

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability.

Cellular immune control of HIV is mediated, in part, by induction of single amino acid mutations that reduce viral fitness, but compensatory mutations limit this effect. Here, we sought to determine if higher order constraints on viral evolution exist, because some coordinately linked combinations of mutations may hurt viability. Immune targeting of multiple sites in such a multidimensionally conserved region might render the virus particularly vulnerable, because viable escape pathways would be greatly restricted.

Effective interaction between charged nanoparticles and DNA.

We investigate the effective interaction mediated by salt ions between charged nanoparticles (NPs) and DNA. DNA is modeled as an infinite cylinder with a constant surface charge in an implicit solvent. Monte Carlo simulations are used to compute the free energy of the system described in the framework of the primitive model of electrolytes, which accounts for excluded volumes of salt ions.

Two-scale Brownian dynamics of suspensions of charged nanoparticles including electrostatic and hydrodynamic interactions.

We propose here a multiscale strategy based on continuous solvent Brownian dynamics (BD) simulations to study the dynamical properties of aqueous suspensions of charged nanoparticles. We extend our previous coarse-graining strategy [V. Dahirel et al.

Ion-mediated interactions in suspensions of oppositely charged nanoparticles.

The structure of oppositely charged spherical nanoparticles (polyions), dispersed in ionic solutions with continuous solvent (primitive model), is investigated by Monte Carlo (MC) simulations, within explicit and implicit microion representations, over a range of polyion valences and densities, and microion concentrations. Systems with explicit microions are explored by semigrand canonical MC simulations, and allow density-dependent effective polyion pair potentials v(alphabeta) (eff)(r) to be extracted from measured partial pair distribution functions. Implicit microion MC simulations are based on pair potentials of mean force v(alphabeta) ((2))(r) computed by explicit microion simulations of two charged polyions, in the low density limit.

Nonspecific DNA-protein interaction: why proteins can diffuse along DNA.

Recent single molecule experiments have reported that DNA binding proteins (DNA-BPs) can diffuse along DNA. This suggests that interactions between proteins and DNA play a role during the target search even far from their specific site on DNA. Here we show by means of Monte Carlo simulations and analytical calculations that there is a counterintuitive repulsion between the two oppositely charged macromolecules at a nanometer range.

Ion-mediated interactions between charged and neutral nanoparticles.

Monte-Carlo simulations are used to study the ion-mediated effective interaction between weakly charged and highly charged nanoparticles in an implicit solvent. Three models of nanoparticles are successively studied, from crude charged hard spheres to dipolar and non-spherical nanoparticles. The analysis of the effective potential revealed that in an electrolyte solution, even a neutral nanoparticle feels an important repulsive force in the presence of a charged nanoparticle, with a typical range similar to the Debye length.

How the excluded volume architecture influences ion-mediated forces between proteins.

The effective interactions between model proteins of various shapes are computed by means of Monte Carlo simulations. In particular, we determine how the modification of the excluded volume architecture influences both entropic and purely electrostatic ion-mediated forces between proteins. We find that interprotein interactions are strongly affected by protein shape, which results in a high decrease of electrostatic screening for typical active site geometries.

Toward the description of electrostatic interactions between globular proteins: potential of mean force in the primitive model.

Monte Carlo simulations are used to calculate the exact potential of mean force between charged globular proteins in aqueous solution. The aim of the present paper is to study the influence of the ions of the added salt on the effective interaction between these nanoparticles. The charges of the model proteins, either identical or opposite, are either central or distributed on a discrete pattern.