402 citations · 8.7k across the 191 of their papers we have counts for
10 papers · 1 filter
Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
C. A. Brackley, M. E. Cates, D. Marenduzzo
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible…
Spontaneous symmetry breaking in active droplets provides a generic route to motility
E. Tjhung, D. Marenduzzo, M. E. Cates
We explore a generic mechanism whereby a droplet of active matter acquires motility by the spontaneous breakdown of a discrete symmetry. The model we study offers a simple represen…
Facilitated diffusion on confined DNA
G. Foffano, D. Marenduzzo, E. Orlandini
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dy…
Bulk rheology and microrheology of active fluids
G. Foffano, J. S. Lintuvuori, A. N. Morozov +3
We simulate macroscopic shear experiments in active nematics and compare them with microrheology simulations where a spherical probe particle is dragged through an active fluid. In…
Sedimentation of Knotted Polymers
Joonas Piili, Davide Marenduzzo, Kimmo Kaski +1
We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show t…
Phase separation and rotor self-assembly in active particle suspensions
J. Schwarz-Linek, C. Valeriani, A. Cacciuto +4
Adding a non-adsorbing polymer to passive colloids induces an attraction between the particles via the `depletion' mechanism. High enough polymer concentrations lead to phase separ…