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We study active agents embedded in bulk or in confinement explicitly considering hydrodynamics and simulating the swimmers via an implementation inspired by the squirmer model. We develop a Dissipative Particle Dynamics scheme for the…
We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability…
We study a harmonic molecule confined to a one--dimensional box with impenetrable walls. We explicitly consider the symmetry of the problem for the cases of different and equal masses. We propose suitable variational functions and compare…
We explore the scattering dynamics of classical Coulomb-interacting clusters of ions confined to a helical geometry. Ion clusters of equally charged particles constrained to a helix can form many-body bound states, i.e. they exhibit stable…
We investigate, using numerical simulations, the conformations of isolated active ring polymers. We find that the their behaviour depends crucially on their size: short rings ($N \lesssim$ 100) are swelled whereas longer rings ($N \gtrsim$…
A simple model of a polymer with long rigid segments which interact via excluded volume repulsions and short ranged attractions is proposed. The coil-globule transition of this model polymer is strongly first order, the globule is…
The $1s^2->1s2p(^1P)$ excitation in confined and compressed helium atoms in either the bulk material or encapsulated in a bubble is shifted to energies higher than that in the free atom. For bulk helium, the energy shifts predicted from…
The collision dynamics of hard spheres and cylindrical pores is solved exactly, which is the minimal model for a regularly porous membrane. Nonequilibrium event-driven molecular dynamics simulations are used to show that the permeability…
Bending of worm-like polymers carries an energy penalty which results in the appearance of a persistence length l such that the polymer is straight on length scales smaller than l and bends only on length scales larger than this length.…
We consider a fully directed self-avoiding walk model on a cubic lattice to mimic the conformations of an infinitely long confined flexible polymer chain; and the confinement condition is achieved by two parallel athermal plates. The…
The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were…
Using Monte Carlo simulation, we analyse the behaviour of two-dimensional hard rods in four different types of geometric confinement: (i) a slit pore where the particles are confined between two parallel walls with homeotropic anchoring;…
We have studied the thermal conductivity of confined superfluids on a bar-like geometry. We use the planar magnet lattice model on a lattice $H\times H\times L$ with $L \gg H$. We have applied open boundary conditions on the bar sides (the…
We analyze the frictionless motion of a point-like particle that slides under gravity on an inverted conical surface. This motion is studied for arbitrary initial conditions and a general relation, valid within 13%, between the periods of…
We consider equilibrium relaxation properties of the end-to-end distance and of principal components in a one-dimensional polymer chain model with nonlinear interaction between the beads. While for the single-well potentials these…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
We study a classical model of thermally fluctuating polymers confined to two dimensions, experiencing a grooved periodic potential, and subject to pulling forces both along and transverse to the grooves. The equilibrium polymer…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
We analyze the free energy for translocation of a polymer from the outside of a spherical vesicle to the inside. The process is assumed to be driven by the adsorption of the polymer on the inner surface of the vesicle. We argue that in the…