Related papers: Theory and simulations for crowding-induced change…
The effects of a dispersed particulate phase on the onset of Rayleigh-B\'enard convection in a fluid layer is studied theoretically by means of a two-fluid Eulerian modelization. The particles are non-Brownian, spherical, with inertia and…
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
The position of a colloidal particle trapped in an external field thermally fluctuates at equilibrium. As is well known, the ambient fluid is not a simple heat bath and the particle mass appears to increase, which influences the mean square…
The Asakura-Oosawa model for colloid-polymer mixtures is studied by Monte Carlo simulations at densities inside the two-phase coexistence region of fluid and solid. Choosing a geometry where the system is confined between two flat walls,…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the…
We investigate the stability of self-propelled particle flocks in the Taylor-Green vortex, a steady vortical flow. We consider a model where particles align themselves to a combination of the orientation and the acceleration of particles…
This study is concerned with behaviour of fluid of monoclonal antibodies (mAbs) when trapped in a confinement represented by rigid spherical obstacles that attract proteins. The antibody molecule is depicted as an assembly of seven hard…
We determine the depletion-induced phase-behavior of hard sphere colloids and interacting polymers by large-scale Monte Carlo simulations using very accurate coarse-graining techniques. A comparison with standard Asakura-Oosawa model…
The velocity relaxation of an impulsively forced spherical particle in a fluid confined by two parallel plane walls is studied using a direct numerical simulation approach. During the relaxation process, the momentum of the particle is…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
Depletion-induced aggregation of rods enhanced by clustering is observed to produce a novel model of attractive pairs of rods separated by a line of spheres in a quasi-2D, vertically-shaken, granular gas of rods and spheres. We show that…
The effect of ring stiffness and pressure on the glassy dynamics of a thermal assembly of two-dimensional ring polymers is investigated using extensive coarse-grained molecular dynamics simulations. In all cases, dynamical slowing down is…
Direct numerical simulation of the gravity-induced settling of finite-size particles in triply-periodic domains has been performed under dilute conditions. For a single solid-to-fluid density ratio of 1.5 we have considered two values of…
We study a one-dimensional system of spatially extended particles, which are fixated to regularly spaced locations by means of elastic springs. The particles are assumed to be driven by a Gaussian noise and to have dissipative,…
Three-dimensional molecular dynamics simulations of dissipative particles (~ 10^6) are carried out for studying the clustering kinetics of granular media during cooling. The inter-connected high particle density regions are identified,…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…