Related papers: Theory and simulations for crowding-induced change…
The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here we introduce the crowded…
We perform extensive Monte Carlo simulations of binary hard-sphere mixtures (with diameter ratios of 5 and 10), to determine the entropic force between (1) a macrosphere and a hard wall, and (2) a pair of macrospheres. The microsphere…
Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies…
Previous studies have shown that the observed temperature anisotropies of protons and alpha particles in the solar wind are constrained by theoretical thresholds for pressure-anisotropy-driven instabilities such as the…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Using simulations between pairs of $\epsilon$-greedy q-learners with one-period memory, this article demonstrates that the potential function of the stochastic replicator dynamics (Foster and Young, 1990) allows it to predict the emergence…
We consider the properties of the diffusion controlled reaction A+B->0 in the steady state, where fixed currents of A and B particles are maintained at opposite edges of the system. Using renormalisation group methods, we explicitly…
For an axisymmetric tokamak plasma, Hamiltonian theory predicts that the orbits of charged particles must stay on invariant tori of conserved energy in the moving frame of reference of a wave that propagates along the torus with a fixed…
By analytically solving some simple models of phase-ordering kinetics, we suggest a mechanism for the onset of non-equilibrium behaviour in colloid-polymer mixtures. These mixtures can function as models of atomic systems; their physics…
Ionic microgel particles in a good solvent swell to an equilibrium size determined by a balance of electrostatic and elastic forces. When crowded, ionic microgels deswell owing to a redistribution of microions inside and outside the…
Molecular-dynamics simulations are presented for two correlation functions formed with the partial density fluctuations of binary hard-sphere mixtures in order to explore the effects of mixing on the evolution of glassy dynamics upon…
Particle Swarm Optimization (PSO) is a nature-inspired meta-heuristic for solving continuous optimization problems. In the literature, the potential of the particles of swarm has been used to show that slightly modified PSO guarantees…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
How frictional effects emerge at the microscopic level in particulate materials remains a challenging question, particularly in systems subject to thermal fluctuations due to the transient nature of interparticle contacts. Here, we directly…
When a suspension freezes, a compacted particle layer builds up at the solidification front with noticeable implications on the freezing process. In a directional solidification experiment of monodispersed suspensions in thin samples, we…
The packing and flow of aspherical frictional particles are studied using discrete element simulations. Particles are superballs with shape $|x|^{s}+|y|^{s}+|z|^{s} = 1$ that varies from sphere ($s=2$) to cube ($s=\infty$), constructed with…
As a generic model for liquid-vapour type transitions in random porous media, the Asakura-Oosawa model for colloid-polymer mixtures is studied in a matrix of quenched spheres using extensive Monte Carlo (MC) simulations. Since such systems…
Using Direct Numerical Simulations (DNS), we examine the effects of Taylor Reynolds number, $R_\lambda$, and Froude number, $Fr$, on the motion of settling, bidisperse inertial particles in isotropic turbulence. Particle accelerations play…
We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…
Starting from the equations of Stokes flow and the mass conservation of particles as determined by shear-induced diffusion, we derive the coupled equations for the dynamics of particle concentration and film thickness for the free-surface…