Related papers: The interplay between phase-separation and gene-en…
The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific,…
The large scale behaviour of a population of cells that grow and interact through the concentration field of the chemicals they secrete is studied using dynamical renormalization group methods. The combination of the effective long-range…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the 3-dimensional…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
The functions of most genetic circuits require sufficient degrees of cooperativity in the circuit components. While mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control,…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
Binary mixtures prepared in an homogeneous phase and quenched into a two-phase region phase-separate via a coarsening process whereby domains of the two phases grow in time. With a numerical study of a spin-exchange model we show that this…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
Biological oscillators coordinate individual cellular components so that they function coherently and collectively. They are typically composed of multiple feedback loops, and period mismatch is unavoidable in biological implementations. We…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
An extension of coupled maps is given which allows for the growth of the number of elements, and is inspired by the cell differentiation problem. The growth of elements is made possible first by clustering the phases, and then by…