Related papers: Modelling spatial constraints and scaling effects …
A system formed by a crowded environment of catalytic obstacles and complex oscillatory chemical reactions is inquired. The obstacles are static spheres of equal radius, which are placed in a random way. The chemical reactions are carried…
Biomolecular condensates form on timescales of seconds in cells upon environmental or compositional changes. Condensate formation is thus argued to act as a mechanism for sensing such changes and quickly initiating downstream processes,…
Surface tension governed by differential adhesion can drive fluid particle mixtures to sort into separate regions, i.e., demix. Does the same phenomenon occur in confluent biological tissues? We begin to answer this question for epithelial…
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding…
The theory of first order density-driven phase transitions with frustration due to the long range Coulomb (LRC) interaction develop on paper I of this series is applied to the following physical systems: i) the low density electron gas ii)…
Different simplified and detailed chemical models and their impact on simulations of combustion regimes initiating by the initial temperature gradient in methane/air mixtures are studied. The limits of the regimes of reaction wave…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge…
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, 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,…
Spontaneous phase separation, or demixing, is important in biological phenomena such as cell sorting. In particle-based models, an open question is whether differences in diffusivity can drive such demixing. While…
Chemical activity is known to affect phase coexistence and coarsening in liquid mixtures, most commonly through reaction-induced changes of intermolecular interactions. Here, we analyze a scenario in which chemical reactions regulate…
The application of an external field often renders empirical criteria for identifying liquid-gas phase transitions ambiguous. Here, we demonstrate that the finite-size scaling of the density profile provides a definitive criterion to…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
This article focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid-liquid…
Collectives of actively-moving particles can spontaneously separate into dilute and dense phases -- a fascinating phenomenon known as motility-induced phase separation (MIPS). MIPS is well-studied for randomly-moving particles with no…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these coacervates play important functional and regulatory roles within biological systems. However, the majority…
Mixtures of several macromolecular species can lead to the formation of higher-order structures that often display non-ideal mixing behavior. In this work, we propose a minimal model of a quaternary system which considers the formation of a…