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Register a new userThe interplay between phase-separation and gene-enhancer communication: a theoretical study
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The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer model which includes regulatory proteins as interacting spherical particles. Our interest is particularly focused on the role played by phase-separation in the formation of molecule aggregates that can join distant regulatory elements, such as gene promoters and enhancers, along the DNA. We find that the overall equilibrium state of the system resulting from the mutual interplay between binding molecules and chromatin can lead, under suitable conditions that depend on molecules concentration, molecule-molecule and molecule-DNA interactions, to the formation of phase-separated molecular clusters allowing robust contacts between regulatory sites. Vice-versa, the presence of regulatory sites can promote the phase-separation process. Different dynamical regimes can generate the enhancer-promoter contact, either by cluster nucleation at binding sites or by bulk spontaneous formation of the mediating cluster to which binding sites are successively attracted. The possibility that such processes can explain experimental live-cell imaging data measuring distances between regulatory sites during time is also discussed.
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We investigate the phase behavior and kinetics of a monodisperse mixture of active (textit{i.e.}, self-propelled) and passive isometric Brownian particles through Brownian dynamics simulations and theory. As in a purely active system, motility of the active component triggers phase separation into a dense and a dilute phase; in the dense phase we further find active-passive segregation, with rafts of passive particles in a sea of active particles. We find that phase separation from an initially disordered mixture can occur with as little as 15 percent of the particles being active. Finally, we show that a system prepared in a suitable fully segregated initial state reproducibly self-assembles an active corona which triggers crystallization of the passive core by initiating a compression wave. Our findings are relevant to the experimental pursuit of directed self-assembly using active particles.
Using computer simulations and dynamic mean-field theory, we demonstrate that fast enough rotation of circle active Brownian particles in two dimensions generates a dynamical clustering state interrupting the conventional motility induced phase separation (MIPS). Multiple clusters arise from the combination of the conventional MIPS cohesion, and the circulating current caused disintegration. The non-vanishing current in non-equilibrium steady states microscopically originates from the motility ``relieved by automatic rotation, which breaks the detailed balance at the continuum level. This mechanism sheds light on the understanding of dynamic clusters formation observed in a variety of active matter systems, and may help examine the generalization of effective thermodynamic concepts developed in the context of MIPS.
The basic ingredients of osmotic pressure are a solvent fluid with a soluble molecular species which is restricted to a chamber by a boundary which is permeable to the solvent fluid but impermeable to the solute molecules. For macroscopic systems at equilibrium, the osmotic pressure is given by the classical vant Hoff Law, which states that the pressure is proportional to the product of the temperature and the difference of the solute concentrations inside and outside the chamber. For microscopic systems the diameter of the chamber may be comparable to the length-scale associated with the solute-wall interactions or solute molecular interactions. In each of these cases, the assumptions underlying the classical vant Hoff Law may no longer hold. In this paper we develop a general theoretical framework which captures corrections to the classical theory for the osmotic pressure under more general relationships between the size of the chamber and the interaction length scales. We also show that notions of osmotic pressure based on the hydrostatic pressure of the fluid and the mechanical pressure on the bounding walls of the chamber must be distinguished for microscopic systems. To demonstrate how the theoretical framework can be applied, numerical results are presented for the osmotic pressure associated with a polymer of N monomers confined in a spherical chamber as the bond strength is varied.
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation through a nanochannel embedded in two dimensions under an applied external field. We examine the translocation time for various ratio of the channel length $L$ to the polymer length $N$. For short channels $Lll N$, the translocation time $tau sim N^{1+ u}$ under weak driving force $F$, while $tausim F^{-1}L$ for long channels $Lgg N$, independent of the chain length $N$. Moreover, we observe a minimum of translocation time as a function of $L/N$ for different driving forces and channel widths. These results are interpreted by the waiting time of a single segment.
Materials undergoing both phase separation and chemical reactions (defined here as all processes that change particle type or number) form an important class of non-equilibrium systems. Examples range from suspensions of self-propelled bacteria with birth-death dynamics, to bio-molecular condensates, or membraneless organelles, within cells. In contrast to their passive counterparts, such systems have conserved and non-conserved dynamics that do not, in general, derive from a shared free energy. This mismatch breaks time-reversal symmetry and leads to new types of dynamical competition that are absent in or near equilibrium. We construct a canonical scalar field theory to describe such systems, with conserved and non-conserved dynamics obeying Model B and Model A respectively (in the Hohenberg-Halperin classification), chosen such that the two free energies involved are incompatible. The resulting minimal model is shown to capture the various phenomenologies reported previously for more complicated models with the same physical ingredients, including microphase separation, limit cycles and droplet splitting. We find a low-dimensional subspace of parameters for which time-reversal symmetry is accidentally recovered, and show that here the dynamics of the order parameter field (but not its conserved current) is exactly the same as an equilibrium system in which microphase separation is caused by long-range attractive interactions.
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