Related papers: The interplay between phase-separation and gene-en…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
Phase separation plays a central role in the emergence of novel functionalities of correlated electron materials. The structure of the mixed-phase states depends strongly on the nonequilibrium phase-separation dynamics, which has so far yet…
A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It is based on the numerical investigation of the counterpart, in lipidic membranes where proteins are diffusing, of the…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
Live-cell imaging experiments have shown that the distal dynamics between enhancers and promoters are unexpectedly rapid and incompatible with standard polymer models. The discordance between the compact static chromatin organization and…
Colloid-polymer mixtures may undergo either fluid-fluid phase separation or gelation. This depends on the depth of the quench (polymer concentration) and polymer-colloid size ratio. We present a real-space study of dynamics in phase…
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
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…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…
Biomolecular phase separation is typically attributed to the polymer physics of long, disordered chains. However, the underlying chemical grammar, i.e. the specific interactions between protein and RNA building blocks, remains poorly…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
A system of two self and mutual interacting ring polymers, close together in space, can display several competing equilibrium phases and phase transitions. Using Monte Carlo simulations and combinatorial arguments on a corresponding lattice…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
The interaction of phase-separating systems with chemical reactions is of great interest in various contexts, from biology to material science. In biology, phase separation is thought to be the driving force behind the formation of…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…