Related papers: Theory and simulations for crowding-induced change…
This paper analyzes the compaction behavior of assemblies composed of soft (elastic) spherical particles beyond the jammed state, using three-dimensional non-smooth contact dynamic simulations. The assemblies of particles are characterized…
The possibility to induce demixing in a colloidal mixture by adding small polymers, or other equivalent depletant agents, is theoretically investigated. By use of Mean Field Theory, suitably generalized to deal with short range effective…
To understand the mechanism of trimethylamine N-oxide (TMAO) induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (Leucine, L2, Serine, S2, Glutamine, Q2, Lysine, K2,…
Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
We investigate the competition between barrier slowing down and proliferation induced superdiffusion in a model of population dynamics in a random force field. Numerical results in $d=1$ suggest that a new intermediate diffusion behaviour…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
In this paper we consider interacting particle systems which are frequently used to model collective behavior in animal swarms and other applications. We study the stability of orientationally aligned formations called flock solutions, one…
We analytically and numerically study the effect of finite spatial boundaries on the Takayasu model of diffusing and aggregating particles with steady monomer input in one dimension. Exact expressions are derived for the steady-state…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
The macroscopic friction of particulate materials often weakens as the flow rate is increased, leading to potentially disastrous intermittent phenomena including earthquakes and landslides. We theoretically and numerically study this…
Distance control in many-particle systems is a fundamental problem in nature. This becomes particularly relevant in systems of active agents, which can sense their environment and react by adjusting their direction of motion. We employ…
Fermi acceleration in a Fermi-Ulam model, consisting of an ensemble of particles bouncing between two, infinitely heavy, stochastically oscillating hard walls, is investigated. It is shown that the widely used approximation, neglecting the…
Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register $\beta$-sheets, the primary structural component of amyloid fibrils, is a first step towards describing \emph{in vivo} protein…
A simple three-dimensional model of a fluid whose constituent particles interact via a short range attractive and long range repulsive potential is used to model the aggregation into large spherical-like clusters made up of hundreds of…
We perform extensive molecular dynamics simulations of dense liquids composed of bidisperse dimer- and ellipse-shaped particles in 2D that interact via repulsive contact forces. We measure the structural relaxation times obtained from the…
The n-person Prisoner's Dilemma is a widely used model for populations where individuals interact in groups. The evolutionary stability of populations has been analysed in the literature for the case where mutations in the population may be…
We study, via DEM simulations, the apparent mass $m$ and loss factor $\eta$ of particle dampers (PD) attached to a vertically driven, single degree of freedom mechanical system. Although many studies focus on $\eta$, less work has been…
We study the stability of the ordered phase of flocking models with a scalar order parameter. Using both the active Ising model and a hydrodynamic description, we show that droplets of particles moving in the direction opposite to that of…