Related papers: Evolved interactions stabilize many coexisting pha…
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.…
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,…
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…
Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
We introduce a method for solving the "inverse" phase equilibria problem: How should the interactions among a collection of molecular species be designed in order to achieve a target phase diagram? Using techniques from convex optimization…
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…
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…
In this paper, we use the cell dynamics method to study the dynamics of phase transformation when three phases exist. The system we study is a two-dimensional system. The system is able to achieve three phases coexistence, which for…
Motivated by the experimental study of Tayebi et al. [Nature Mater. 11, 1074 (2012)] on phase separation of stacked multi-component lipid bilayers, we propose a model composed of stacked two-dimensional Ising spins. We study both its static…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
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…
We investigate the emergence of sustained spatio-temporal behaviors in reaction-phase separation systems. We focus on binary systems, in which either one or both species can phase separate, and we discuss the stability of the homogeneous…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
Active matter is not only indispensable to our understanding of diverse biological processes, but also provides a fertile ground for discovering novel physics. Many emergent properties impossible for equilibrium systems have been…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
We demonstrate the emergence of self-organized structures in the course of the relaxation of an initially excited, dissipative and finite chain of interacting particles in a periodic potential towards its many particle equilibrium…