Related papers: Robust microphase separation through chemical reac…
Phase separation routinely occurs in both living and synthetic systems. These phases are often complex and distinguished by features including crystallinity, nematic order, and a host of other nonconserved order parameters. For systems at…
Various biological and chemical processes lead to the nucleation and growth of non-wetting fluid bubbles within the pore space of a granular medium, such as the formation of gas bubbles in liquid-saturated lake-bed sediments. In…
The stochastic kinetics of BRN are described by a chemical master equation (CME) and the underlying laws of mass action. The CME must be usually solved numerically by generating enough traces of random reaction events. The resulting…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small…
Co-existence of phase segregation and \emph{interconversion} or \emph{isomerization} reaction among molecular species leads to fascinating structure formation in biological and chemical world. Using Monte Carlo simulations of the prototype…
Some results are presented on how oscillation is inherited by chemical reaction networks (CRNs) when they are built in natural ways from smaller oscillatory networks. The main results describe four important ways in which a CRN can be…
RNA-binding proteins form biomolecular condensates with RNA through phase separation, playing crucial roles in various cellular processes. While intrinsically disordered regions (IDRs) are key drivers of phase separation, additional factors…
Quenched or frozen-in structural disorder is ubiquitous in real experimental systems. Much of the progress is achieved in understanding the phase separation of such systems using the diffusion-driven coarsening in Ising model with quenched…
The aim of this paper is to discuss the mathematical modeling of Brownian active particle systems, a recently popular paradigmatic system for self-propelled particles. We present four microscopic models with different types of repulsive…
Biomolecular condensates are complex droplets comprising diverse molecules that interact using various mechanisms. Condensation is often driven by short-ranged attraction, but net charges can also mediate long-ranged repulsion. Using…
Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
These lecture notes describe a basic theory of chemically active droplets, which are droplets kept away from equilibrium by driven chemical reactions. The notes assume a basic familiarity with equilibrium thermodynamics of phase separation,…
Usually, we expect large particles to sediment faster than small of the same material. Contrary to this intuition, we report a dynamical competition between sedimentation and phase ordering which leads to smaller particles settling faster…
Suspensions of purely repulsive but self-propelled Brownian particles might undergo phase separation, a phenomenon that strongly resembles the phase separation of passive particles with attractions. Here we employ computer simulations to…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
The phase separation mechanism of a binary liquid mixture off-critically quenched in its miscibility gap is nucleation and growth, its homogeneous phase reaching a metastable equilibrium state. The successive stages of growth of the…
Complex behavior in glassforming liquids is associated with formation of a mosaic of different structures. Using bond order parameters together with topological characteristics of the bond network, we show that in the mosaic of crystalline…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…