Related papers: The interplay between phase-separation and gene-en…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Differences in activities in colloidal particles are sufficient to drive phase separation between active and passive (or less active) particles, even if they have only excluded volume interactions. In this paper, we study the phase…
Phase separation drives the formation of biomolecular condensates in cells, which comprise many components and sometimes possess multiple phases. The equilibrium physics of phase separation is well understood, but many components in…
We study the problem of phase separation in systems with a positive definite order parameter, and in particular, in systems with absorbing states. Owing to the presence of a single minimum in the free energy driving the relaxation kinetics,…
We study the effect of a coupling between two motor domains in highly-processive motor protein complexes. A simple stochastic discrete model, in which the two parts of the protein molecule interact through some energy potential, is…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
We investigate synchronization effects in quantum self-sustained oscillators theoretically using the micromaser as a model system. We use the probability distribution for the relative phase as a tool for quantifying the emergence of…
Contact inhibition is the process by which cells switch from a motile growing state to a passive and stabilized state upon touching their neighbors. When two cells touch, an adhesion link is created between them by means of transmembrane…
The formation of polarized signaling domains on cell membranes is a fundamental example of biological pattern formation. While such patterns resemble structures from equilibrium phase separation, they are intrinsically non-equilibrium,…
Letting free polymers diffuse from solution into a crosslinked polymer gel is often a crucial processing step in the synthesis of multiphase polymer-based gels, e.g., core-shell microgels. Here we use coarse-grained molecular dynamics…
A driven diffusive model of three types of particles that exhibits phase separation on a ring is introduced. The dynamics is local and comprises nearest neighbor exchanges that conserve each of the three species. For the case in which the…
There are rich emergent phase behaviors in non-equilibrium active systems. Flocking and clustering are two representative dynamic phases. The relationship between these two phases is still unclear. In the paper, we numerically investigate…
A general quantitative measure of the tendency towards phase separation is introduced for systems exhibiting phase transitions or crossovers controlled by charge carrier concentration. This measure is devised for the situations when the…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
We consider a system of clusters made of elementary building blocks, monomers, and evolving via collisions between diffusing monomers and immobile composite clusters. In our model, the cluster-monomer collision can lead to the attachment of…
We show how to construct a reduced description of interacting genes in noisy, small regulatory networks using coupled binary "spin" variables. Treating both the protein number and gene expression state variables stochastically and on equal…
Elastic interactions arising from a difference of lattice spacing between two coherent phases can have a strong influence on the phase separation (coarsening) of alloys. If the elastic moduli are different in the two phases, the elastic…