Related papers: Theory and simulations for crowding-induced change…
We propose a new coarse-grained model for the description of liquid-vapor phase separation of colloid-polymer mixtures. The hard-sphere repulsion between colloids and between colloids and polymers, which is used in the well-known…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
{\alpha}-synuclein ({\alpha}-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of…
We study the equilibrium behaviour of a mixture of monodisperse hard sphere colloids and polydisperse non-adsorbing polymers at their $\theta$-point, using the Asakura-Oosawa model treated within the free-volume approximation. Our focus is…
We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we…
Experiments show that macromolecular crowding modestly reduces the size of intrinsically disordered proteins (IDPs) even at volume fraction ($\phi$) similar to that in the cytosol whereas DNA undergoes a coil-to-globule transition at very…
We study flexible polymer macromolecules in a crowded (porous) environment, modelling them as self-attracting self-avoiding walks (SASAW) on site-diluted percolative lattices in space dimensions d=2, 3. The influence of stretching force on…
Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While…
The influence of confinement, due to flat parallel structureless walls, on phase separation in colloid-polymer mixtures, is investigated by means of grand-canonical Monte Carlo simulations. Ultra-thin films, with thicknesses between…
At low densities, with decreasing temperatures, in symmetric nuclear matter alpha-particles are formed, which eventually give raise to a quantum condensate with four-nucleon alpha-like correlations (quartetting). Starting with a model of…
How fast a post-translational nascent protein escapes from the ribosomal exit tunnel is relevant to its folding and protection against aggregation. Here, by using Langevin molecular dynamics, we show that non-local native interactions help…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
We derive an analytical pair potential of mean force for Brownian molecules in the liquid-state. Our approach accounts for many-particle correlations of crowding particles of the liquid, and for diffusive transport across the spatially…
By combining the nonconserved spin-flip dynamics driving ferromagnetic ordering with the conserved Kawasaki-exchange dynamics driving phase segregation, we perform Monte Carlo simulations of the nearest neighbor Ising model. Such a set up…
In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to…
As first explained by the classic Asakura-Oosawa (AO) model, effective attractive forces between colloidal particles induced by depletion of nonadsorbing polymers can drive demixing of colloid-polymer mixtures into colloid-rich and…
Diffusion in the crowded environments of the biological membranes or materials interfaces often involves intermittent binding to surface proteins or defects. To account for this situation we study a 2-dimensional lattice gas in a field of…
A model for diffusion-controlled spherical particle growth is presented and solved numerically, showing how, on cooling at sufficient rate from a given fraction solid, growth velocity first increases, and then decreases rapidly when solute…
The phase behavior of stabilized dispersions of macromolecules is most easily described in terms of the effective interaction between the centers of mass of solute particles. For molecules like polymer chains, dendrimers, etc., the…