Related papers: The interplay between phase-separation and gene-en…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a…
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long distance regulatory interactions. The mechanistic basis…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
The phase behavior of colloid-polymer mixtures, and of solutions of globular proteins, is often interpreted in terms of a simple model of hard spheres with short-ranged attraction. While such a model yields a qualitative understanding of…
Biological mixtures such as the cytosol may consist of thousands of distinct components. There is now a substantial body of evidence showing that, under physiological conditions, intracellular mixtures can phase separate into spatially…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
Proteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Phase separation plays an role in determining the self-assembly of biological and soft-matter systems. In biological systems, liquid-liquid phase separation inside a cell leads to the formation of various macromolecular aggregates. The…
Given the wide range of length scales, the analysis of polymer systems often requires coarse-graining, for which various levels of description may be possible depending on the phenomenon under consideration. Here, we provide a super-coarse…
Understanding the differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We develop a theoretical framework to quantify the underlying potential landscape and biological…
Phase separation dynamics with an initially non-uniform concentration are studied. Critical and off-critical behavior is observed simultaneously. A mechanism for an expanding phase separated region is demonstrated and the time dependence of…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membrane-less compartments in order to confine and localize particles like proteins. In many cases these particles are bound to fluctuating…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…