Related papers: Coarse-graining bistability with the Martini force…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
We present mathematically rigorous expressions for the residence-time and first-passage-time distributions of a periodically forced Brownian particle in a bistable potential. For a broad range of forcing frequencies and amplitudes, the…
A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…
In recent years, active Brownian particles have emerged as a prominent model system for comprehending the behaviors of active matter, wherein particles demonstrate self-propelled motion by harnessing energy from the surrounding environment.…
We study the overdamped motion of a particle in a bistable potential subject to the action of a bichromatic force and additive noise, within the context of the vibrational resonance phenomenon. Under appropriate conditions, we obtain…
Observing spontaneous velocity ordering or flocking during motility induced phase separation (MIPS) in a system of spherical active Brownian particles without alignment interaction is challenging. We take up this problem by performing…
In this work we identify and investigate a novel bifurcation in conserved systems. This secondary bifurcation stops active phase separation in its nonlinear regime. It is then either replaced by an extended, system-filling, spatially…
A model for the dynamical evolution of a granular binary mixture is analyzed. This system is submitted to a tapping procedure, similarly to what is done in real experiments. In the weak vibration limit, an effective dynamics for the tapping…
A set of interacting vortices in $2D$ in the presence of a substrate with square symmetry and at filling ratio $1$ can display a low temperature solid phase where only one of the reciprocal lattice vectors of the substrate is…
We consider the application of fluctuation relations to the dynamics of coarse-grained systems, as might arise in a hypothetical experiment in which a system is monitored with a low-resolution measuring apparatus. We analyze a stochastic,…
The equilibrium properties of a system of passive diffusing particles in an external magnetic field are unaffected by the Lorentz force. In contrast, active Brownian particles exhibit steady-state phenomena that depend on both the strength…
We present experimental results on slow flow properties of a granular assembly confined in a vertical column and driven upwards at a constant velocity V. For monodisperse assemblies this study evidences at low velocities ($1<V<100 \mu m/s$)…
We coarse-grain a model of closely-packed ellipses that can vary their aspect ratio to derive continuum equations for materials comprising confluent deformable particles such as epithelial cell layers. We show that contractile nearest…
We develop a minimal theoretical model that reveals a structured steady-state flux field with four alternating local circulation, a phenomenon we refer to as quadrupolar gyration. A passive Brownian particle is confined to move in a…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
Transport in a one-dimensional symmetric device can be activated by the combination of thermal noise and a bi-harmonic drive. For the study case of an overdamped Brownian particle diffusing on a periodic one-dimensional substrate, we…
We examine the dynamics of two-dimensional colloidal systems using numerical simulations of a system with a drive applied to a thin region in the middle of the sample to produce a local shear. For a monodisperse colloidal assembly, we find…
Nonlinearities can have a profound influence on the dynamics and equilibrium properties of discrete lattice systems. The simple case of two coupled modes with self-nonlinearities gives rise to the rich bosonic Josephson effects. In…
Cohesive granular materials are found in many natural and industrial environments, but experimental platforms for exploring the innate mechanical properties of these materials are often limited by the difficulty of adjusting cohesion…