arXiv subjects

Marie Jardat

Publications and source records attributed to Marie Jardat.

16 recordsLinked to original sources

arXiv2025

Chemically active droplets in crowded environments

Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of proteins that switch between attractive and repulsive states via nonequilibrium chemical reactions. While field-based simulations have provided insights into their behavior, these coarse-grained approaches fail to capture molecular-scale effects, particularly in crowded cellular environments. Macromolecular crowding, a key feature of intracellular organization, strongly influences molecular transport within condensates, yet its quantitative impact remains underexplored. This study investigates the interplay between chemically active droplets and crowders by using particle-based models, that provide molecular insight, and a field-based model, that complements this picture. Surprisingly, crowding reduces droplet size while expanding the overall dense phase volume, challenging equilibrium-based expectations. This effect arises from the interplay between depletion interactions, diffusion hindrance, and nonequilibrium particle fluxes. Our findings provide a step towards a more comprehensive understanding of chemically active droplets in complex, realistic cellular environments.

cond-mat.soft↗

arXiv2025

Control of encounter kinetics by chemically active droplets

Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and stability influenced by non-equilibrium chemical reactions. While condensates are frequently considered optimized nanoreactors that enhance molecular encounters, their actual impact on reaction kinetics remains unclear due to competing effects such as diffusion hindrance, and random trapping in non-specific condensates. In this study, we develop a microscopic, stochastic model for chemically active droplets, incorporating reaction-driven modulation of protein interactions. Using Brownian dynamics simulations, we investigate how protein interactions and active coupling to a free energy reservoir influence phase separation, molecular transport and reaction kinetics. We demonstrate that the intensity of the chemical drive governs surface dynamics, generating fluxes that modulate bimolecular reaction rates. Comparing active emulsions to homogeneous systems, we reveal that condensates can either accelerate or decelerate molecular encounters. Our findings provide key insights into the role of biomolecular condensates as potential regulators of intracellular reaction kinetics.

cond-mat.soft↗

arXiv2024

Active droplets controlled by enzymatic reactions

The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple generic model to study the interplay between two enzyme populations and a two-state protein. In one state, the protein forms condensed droplets through attractive interactions, while in the other state, the proteins remain dispersed. Each enzyme catalyzes the production of one of these two protein states only when reactants are in its vicinity. A key feature of our model is the explicit representation of enzyme trajectories, capturing the fluctuations in their local concentrations. The spatially dependent growth rate of droplets naturally arises from the stochastic motion of these explicitly modeled enzymes. Using two complementary numerical methods, (1) Brownian Dynamics simulations, and (2) a hybrid method combining Cahn-Hilliard-Cook diffusion equations with Brownian Dynamics for the enzymes, we investigate how enzyme concentration and dynamics influence the evolution with time, and the steady-state number and size of droplets. Our results show that the concentration and diffusion coefficient of enzymes govern the formation and size-selection of biocondensates.

cond-mat.soft↗

arXiv2024

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 (LLPS) 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). Chromatin particles are trapped in a harmonic potential to reproduce the coil and globular phases of an isolated polymer chain. We investigate the role of the droplet material B on the radius of gyration of this polymer and find that this radius varies nonmonotonically with respect to the volume fraction of B. This behavior is reminiscent of a phenomenon known as $\textit{co-non-solvency}$: a polymer chain in good solvent (S) may collapse when a second good solvent (here B) is added in low quantity, and expand at higher B concentration. Additionally, the presence of finite-size effects on the coil-globule transition results in a qualitatively different impact of the droplet material on polymers of various sizes. In the context of genetic regulation, our results suggest that the size of chromatin domains and the quantity of condensate proteins are key parameters to control whether chromatin may respond to an increase of the quantity of chromatin-binding proteins by condensing or expanding.

physics.bio-ph↗

arXiv2024

Microscopic and stochastic simulations of chemically active droplets

Biomolecular condensates play a central role in the spatial organization of living matter. Their formation is now well understood as a form of liquid-liquid phase separation that occurs very far from equilibrium. For instance, they can be modeled as active droplets, where the combination of molecular interactions and chemical reactions result in microphase separation. However, so far, models of chemically active droplets are spatially continuous and deterministic. Therefore, the relationship between the microscopic parameters of the models and some crucial properties of active droplets (such as their polydispersity, their shape anisotropy, or their typical lifetime) is yet to be established. In this work, we address this question computationally, using Brownian dynamics simulations of chemically active droplets: the building blocks are represented explicitly as particles that interact with attractive or repulsive interactions, depending on whether they are in a droplet-forming state or not. Thanks to this microscopic and stochastic view of the problem, we reveal how driving the system away from equilibrium in a controlled way determines the fluctuations and dynamics of active emulsions.

cond-mat.soft↗

arXiv2023

Enhanced diffusion of tracer particles in nonreciprocal mixtures

We study the diffusivity of a tagged particle in a binary mixture of Brownian particles with non-reciprocal interactions. Numerical simulations reveal that, for a broad class of interaction potentials, non-reciprocity can significantly increase the effective 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; (ii) a reduced two-body description, which is exact at leading order in the density of particles. The latter reveals that diffusion enhancement can be attributed to the formation of transiently propelled dimers of particles, whose cohesion and speed are controlled by the non-reciprocal interactions.

cond-mat.soft↗

arXiv2023

On analytical theories for conductivity and self-diffusion in concentrated electrolytes

Describing analytically the transport properties of electrolytes, such as their conductivity or the self-diffusion of the ions, has been a central challenge of chemical physics for almost a century. In recent years, this question has regained some interest in light of Stochastic Density Field Theory (SDFT) -- an analytical framework that allows the approximate determination of density correlations in fluctuating systems. In spite of the success of this theory to describe dilute electrolytes, its extension to concentrated solutions raises a number of technical difficulties, and requires simplified descriptions of the short-range repulsion between the ions. In this article, we discuss recent approximations that were proposed to compute the conductivity of electrolytes, in particular truncations of Coulomb interactions at short distances. We extend them to another observable (the self-diffusion coefficient of the ions) and compare them to earlier analytical approaches, such as the mean spherical approximation and mode-coupling theory. We show how the treatment of hydrodynamic effects in SDFT can be improved, that the choice of the modified Coulomb interactions significantly affects the determination of the properties of the electrolytes, and that comparison with other theories provides a guide to extend SDFT approaches in this context.

cond-mat.soft↗

arXiv2023

Isotropic active colloids: explicit vs. 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. The colloid catalyzes a chemical reaction in its vicinity, which results in a local phase separation of solute particles, and the density fluctuations of solute particles cause the enhanced diffusion of the colloid. In this paper, we investigate an assembly of such active particles, using (i) an explicit model, where the microscopic dynamics of the solute particles is accounted for; and (ii) an implicit model, whose parameters are inferred from the explicit model at infinite dilution. In the explicit solute model, the effective diffusion coefficient of the active colloids strongly decreases with density, an effect which is not captured by the derived implicit model. This suggests that classical models, which usually decouple pair interactions from activity, fail to describe collective dynamics in active colloidal systems driven by solute-solute interactions.

cond-mat.soft↗

arXiv2022

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. Our analytical result is confronted to results from Brownian dynamics simulations. The agreement with numerical simulations is very good even for high densities. We show how the diffusivity of tracers can be affected by the activity of a dense environment of soft particles that may represent polymer coils -- a result that could be of relevance in the interpretation of measurements of diffusivity in biological media. Finally, our analytical result is general and can be applied to the diffusion of tracers coupled to different types of fluctuating environments, provided that their evolution equations are linear and that the coupling between the tracer and the bath is weak.

cond-mat.soft↗

arXiv2022

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. Using numerical simulations, we thoroughly investigate the conditions under which activity occurs, and we establish a state diagram for the activity of the colloid as a function of the parameters of the model. We use the generated data to unravel a key observable that controls the existence and the intensity of activity: the filling fraction of the reaction area. Remarkably, we finally show that propulsion also occurs in three-dimensional geometries, which confirms the interest of this mechanism for experimental applications.

cond-mat.soft↗

arXiv2021

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. Here, we propose a minimal model of an isotropic colloid in a bath of solute particles that interact with each other. These interactions lead to a spontaneous phase transition close to the colloid, to directed motion of the colloid over very long timescales and to significantly enhanced diffusion, in spite of the crowding induced by solute particles. We determine the range of parameters where this effect is observable in the model, and we propose an effective Langevin equation that accounts for it and allows one to determine the different contributions at stake in self-propulsion and enhanced diffusion.

cond-mat.soft↗

arXiv2020

Can we describe charged nanoparticles with electrolyte theories? Insight from mesoscopic simulation techniques

Electrolyte theories enable to describe the structural and dynamical properties of simple electrolytes in solution, such as sodium chloride in water. Using these theories for aqueous solutions of charged nanoparticles is a straightforward route to extract their charge and size from experimental data. Nevertheless, for such strongly asymmetric electrolytes, the validity of the underlying approximations have never been properly challenged with exact simulation results. In the present work, well established mesoscopic numerical simulations are used to challenge the ability of advanced electrolyte theories to predict the electrical conductivity of suspensions of charged nanoparticles, in the salt-free case. The theories under investigation are based on the Debye-Fuoss-Onsager treatment of electrolyte transport. When the nanoparticles are small enough (about one nanometer large), the theoretical results agree remarkably well with the simulation ones, even in the high concentration regime (packing fraction of in nanoparticles larger than 3$\%$ ). Strikingly, for highly charged nanoparticles, the theory is able to capture the non-monotonic variation of the ratio of the electrical conductivity to its value at infinite dilution (ideal value) as a function of the concentration. However, the tested theories fail to describe the conductivity of suspensions containing larger nanoparticles ({\em e.g.} of diameter $4$~nm). Finally, only small charged nanoparticles can be considered as {\em ions}, as far as electrolyte theories are concerned.

cond-mat.soft↗

arXiv2020

Coarse-grained Models of Aqueous Solutions of Polyelectrolytes: Significance of Explicit Charges

The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its 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. Our present study compares the ability of different kinds of coarse-grained models: (i)~to reproduce the structure of an atomistic model of a polyelectrolyte (the sodium polyacrylate), (ii)~to reproduce the variations of this structure with the number of monomers and with the concentration of the different species. We show that the adequate scalings of the gyration radius of the polymer~$R_{\rm g}$ with the number of monomers~$N$ and with the box size~$L_{\rm box}$ are only obtained, first, if the monomer charges and the counterions are explicitely described, and second, if an attractive Lennard-Jones contribution is added to the interaction between distant monomers. Also, we show that implicit ion models are relevant only to the high electrostatic screening regime.

cond-mat.soft↗

arXiv2018

Hydrodynamic interactions between solutes in multiparticle collision dynamics

Multiparticle collision dynamics (MPCD) enables to simulate fluid dynamics including both hydrodynamics and thermal fluctuations. Its main use concerns complex fluids, where the solvent interacts with concentrated solutes, may they be colloidal particles, polymers or electrolytes. A key difficulty concerns the way one couples the fluid to the solute particles, without losing the key advantages of the MPCD method in term of computational efficiency. In this paper, we investigate the dynamical properties of solutes that are coupled to the fluid within the collision step, {\em i.e.} when local momentum exchange between fluid particles occurs. We quantify how the volume where momentum exchange is performed (the size of the collision cells) constrains the hydrodynamic size of the solute. Moreover, we show that this volume should be taken smaller than the structural size of the solutes. Within these constraints, we find that the hydrodynamic properties of a 1-1 electrolyte solution are similar to the behaviour predicted by the Fuoss-Onsager theory of electrolyte dynamics, and we quantify the limitations of the theory for 2-1 and 2-2 electrolytes. However, it is also clear that mapping the diffusion time scale to that of a real system cannot be done quantitatively with this methodology.

cond-mat.soft↗

arXiv2018

Computation of the Hydrodynamic Radius of Charged Nanoparticles from Non-equilibrium Molecular Dynamics

We have used non-equilibrium molecular dynamics to simulate the flow of water molecules around a charged nanoparticle described at the atomic scale. These non-equilibrium 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. We show that both lead to an adequate control of the temperature of the system. To deduce the hydrodynamic radius of the nanoparticle we have employed a partial thermostat, which exploits the cylindrical symmetry of the flow field. Thereby, only a part of the simulation box far from the nanoparticle is thermostated. We have taken into account the finite concentration of the nanoparticle by using the result of Hasimoto (J. Fluid. Mech. {\bf 1959}, {\it 5}, 317-328 ) for the friction force in a periodic cubic array of spheres. We have focused on the case of polyoxometalate ions, which are inorganic charged nanoparticles. It appears that, for a given structure of the nanoparticle at the atomic level, the hydrodynamic radius significantly increases with the nanoparticle's charge, a phenomenon that had not been quantified so far using molecular dynamics. The presence of an added salt only slightly modifies the hydrodynamic radius.

cond-mat.soft↗

arXiv2009

Non-specific DNA-protein interaction: Why proteins can diffuse along DNA

The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between proteins and DNA play a role during the target search even far from the specific site. It is unclear how these non-specific interactions optimize the search process, and how the protein structure comes into play. Each nucleotide being negatively charged, one may think that the positive surface of DNA-BPs should electrostatically collapse onto DNA. Here we show by means of Monte Carlo simulations and analytical calculations that a counter-intuitive repulsion between the two oppositely charged macromolecules exists at a nanometer range. We also show that this repulsion is due to a local increase of the osmotic pressure exerted by the ions which are trapped at the interface. For the concave shape of DNA-BPs, and for realistic protein charge densities, we find that the repulsion pushes the protein in a free energy minimum at a distance from DNA. As a consequence, a favourable path exists along which proteins can slide without interacting with the DNA bases. When a protein encounters its target, the osmotic barrier is completely counter-balanced by the H-bond interaction, thus enabling the sequence recognition.

q-bio.BM↗