A many-body Hamiltonian for nanoparticles immersed in a polymer solution

Non-monotonic phase behaviour of a mixture containing non-adsorbing particles and polymerising rod-like molecules

HYPOTHESIS

Previous works have shown that many-body interactions induced by dispersants with increasing correlation length will generate a diminishing two-phase region [Soft Matter 14, 6921 (2018)]. We conjecture that the attenuation of the depletion attraction due to many-body interactions is a ubiquitous phenomenon in medium-induced interactions. We propose mixtures of colloidal particles and rod-like polymers as a feasible experimental system for verifying these predictions, since the intra-molecular correlations are not screened in a good solvent for rod-like polymers as they are in flexible polymers. The length of the rods can grow and become the dominant length scale that determines the range of the depletion interactions for the imbedded non-adsorbing particles. Simulations: We study many-body depletion forces induced by polymerizing rod-like polymers on spherical non-adsorbing colloids, using Metropolis Monte Carlo simulations. We also employ a simple mean-field theory to further justify our numerical predictions.

FINDINGS

We demonstrate that the phase diagram displays the same qualitative features that have previously been predicted by many-body theory, for mixtures containing flexible polymers under theta solvent conditions. The contraction of the particle two-phase region that we observe, as the correlation length increases beyond some specific value, could be a signature of the weakening of the depletion caused by many-body effects.

Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling

This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this work, we investigate the interplay of these two mechanisms with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime in which the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixing.

Preferential Localization of the Bacterial Nucleoid

Prokaryotes do not make use of a nucleus membrane to segregate their genetic material from the cytoplasm, so that their nucleoid is potentially free to explore the whole volume of the cell. Nonetheless, high resolution images of bacteria with very compact nucleoids show that such spherical nucleoids are invariably positioned at the center of mononucleoid cells. The present work aims to determine whether such preferential localization results from generic (entropic) interactions between the nucleoid and the cell membrane or instead requires some specific mechanism, like the tethering of DNA at mid-cell or periodic fluctuations of the concentration gradient of given chemical species. To this end, we performed numerical simulations using a coarse-grained model based on the assumption that the formation of the nucleoid results from a segregative phase separation mechanism driven by the de-mixing of the DNA and non-binding globular macromolecules. These simulations show that the abrupt compaction of the DNA coil, which takes place at large crowder density, close to the jamming threshold, is accompanied by the re-localization of the DNA coil close to the regions of the bounding wall with the largest curvature, like the hemispherical caps of rod-like cells, as if the DNA coil were suddenly acquiring the localization properties of a solid sphere. This work therefore supports the hypothesis that the localization of compact nucleoids at regular cell positions involves either some anchoring of the DNA to the cell membrane or some dynamical localization mechanism.

Many-body effects in a binary nano-particle mixture dispersed in ideal polymer solutions

A new mean-field theory is developed to treat a binary mixture of nanoparticles imbedded in a polydisperse polymer solution. The theory is based on a many-body polymer-mediated potential of mean force (PMF) between the particles and remains accurate even in the protein regime, where the particles' diameters cannot necessarily be considered large compared to the polymer radius of gyration. As implemented here, the theory is strictly valid for dilute to semi-dilute polymer solutions near the theta temperature (the so-called theta regime) or when the range of the PMF is strongly affected by the polymer size. For non-adsorbing particles, this is the same regime where the celebrated Asakura-Oosawa (AO) model is often used. Unlike the traditional AO model, however, our approach includes polymer flexibility and is accurate in the protein regime. We use the theory to calculate phase diagrams for a binary mixture of unequal-sized particles, both adsorbing and non-adsorbing. To test the theory, we carry out comparisons with simulations and obtained good quantitative agreement, which gives support to its accuracy. On the other hand, the oft-used approach assuming pairwise-additive potentials of mean force produce quantitatively (and sometime qualitatively) different phase diagrams.

Many-body depletion forces of colloids in a polydisperse polymer dispersant in the long-chain limit

We study a system of spherical non-adsorbing particles immersed in a polydisperse polymer fluid. We derive an analytic expression for the many-body depletion interactions between the colloidal particles in the limit of very long chains. We argue that this expression is essentially exact for long chains and justify this using explicit simulations. In this way we are able to elucidate the profound effect of many-body interactions on the particle thermodynamics. We show that using truncated 2-body depletion interactions leads to strong particle segregation, while the complete many-body description predicts that the total depletion force becomes weak so that the system approximates one which interacts via a so-called Kac potential. This implies that the depletion interactions can be described using mean-field theory. We show that many-body effects cause a significant contraction of the 2-phase region of the particle dispersion. We also investigate the system approaching the (tricritical) θ point, which terminates the line of first-order critical points of the polymer dispersion in a poor solvent and show that many-body effects suppress particle phase transitions.

Many-body interactions between charged particles in a polymer solution: the protein regime

We study the phase behavior of charged particles in electrolyte solutions wherein non-adsorbing polymers are added to provide an attractive depletion interaction. The polymer has a radius of gyration similar to that of the particle radius, which causes significant many-body effects in the effective polymer mediated interaction between particles. We use a recently developed analytical theory, which gives a closed expression for the full depletion interaction, accounting for all orders of many-body terms in the potential of mean force. We compare with simulations of an explicit polymer model and show that the potential of mean force provides an accurate and computationally efficient description for the charged particle/polymer mixture, over a range of electrolyte concentrations. Furthermore, we demonstrate that the usual pair potential approach is highly inaccurate for these systems. A simple simulation method is used to estimate the limits of stability of the mixture. The pair approximation is shown to predict a much greater region of instability compared with the many-body treatment, due to its overestimation of the polymer depletion effect.