Related papers: Theory and simulations for crowding-induced change…
The study deals with the Payne effect (a substantial decrease in the storage modulus of a particle-reinforced elastomer with an increase in the amplitude of mechanical oscillations). The influence of temperature, concentration of filler and…
In this study, inspired by the work of K. Nakazato and K. Kitahara [Prog. Theor. Phys. 64, 2261 (1980)], we consider the theoretical problem of tracer particle diffusion in an environment of diffusing hardcore interacting crowder particles.…
30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully…
To rigorously model fast ions in fusion plasmas, a non-Maxwellian equilibrium distribution must be used. In the work, the response of high-energy alpha particles to electrostatic turbulence has been analyzed for several different tokamak…
Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We…
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
We investigate the effect of temperature on $\alpha$-particle clustering in the diluted nucleus $^{16}\text{O}$ using the multi-constrained finite-temperature relativistic Hartree-Bogoliubov model with the DD-ME2 interaction. At a critical…
We classify and predict the asymptotic dynamics of a class of swarming models. The model consists of a conservation equation in one dimension describing the movement of a population density field. The velocity is found by convolving the…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
Active matter with local polar or nematic order is subject to the well-known Simha-Ramaswamy instability. It is so far unclear how, despite this instability, biological tissues can undergo robust active anisotropic deformation during animal…
We explore the consequences of the excluded volume interaction of hard spheres at high densities and present a theory for excited granular materials. We first demonstrate that, in the presence of gravity, the granular density crosses over…
We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding…
There is considerable evidence for widespread subsonic turbulence in galaxy clusters, most notably from {\it Hitomi}. Turbulence is often invoked to offset radiative losses in cluster cores, both by direct dissipation and by enabling…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
We study theoretically and numerically how hard frictionless particles in random packings can rearrange. We demonstrate the existence of two distinct unstable non-linear modes of rearrangement, both associated with the opening and the…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
We extensively investigated the critical behavior of mixtures of colloids and polymers via the two-component Asakura-Oosawa model and its reduction to a one-component colloidal fluid using accurate theoretical and simulation techniques. In…
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a…
Phase separation of colloid-polymer mixtures, described by the Asakura-Oosawa (AO) model, confined in a thin slit pore is studied by grand-canonical Monte Carlo simulation. While one wall is a hard wall for both particles, at the other wall…
We demonstrate that the modulation instability of the zone boundary mode in a finite (periodic) Fermi-Pasta-Ulam chain is the necessary but not sufficient condition for the efficient energy transfer by localized excitations. This transfer…