The linked cell list algorithm is an essential part of molecular simulation
software, both molecular dynamics and Monte Carlo. Though it scales linearly
with the number of particles, there has been a constant interest in increasing
its efficiency, because a large part of CPU time is spent to identify the
interacting particles. Several recent publications proposed improvements to the
algorithm and investigated their efficiency by applying them to particular
setups. In this publication we develop a general method to evaluate the
efficiency of these algorithms, which is mostly independent of the parameters
of the simulation, and test it for a number of linked cell list algorithms. We
also propose a combination of linked cell reordering and interaction sorting
that shows a good efficiency for a broad range of simulation setups.Comment: Submitted to Computer Physics Communications on 22 December 2009,
still awaiting a referee repor
Structural properties of brushes which are composed of weak acidic and basic polyelectrolytes are studied in the framework of a particle-based approach that implicitly accounts for the solvent quality. Using a semi-grandcanonical partition function in the framework of the Single-Chain-in-Mean-Field (SCMF) algorithm, the weak polyelectrolyte is conceived as a supramolecular mixture of polymers in different dissociation states, which are explicitly treated in the partition function and sampled by the SCMF procedure. One obtains a local expression for the equilibrium acid-base reaction responsible for the regulation of the charged groups that is also incorporated to the SCMF sampling. Coupled to a simultaneous treatment of the electrostatics, the approach is shown to capture the main features of weak polyelectrolyte brushes as a function of the bulk pH in the solution, the salt concentration, and the grafting density. Results are compared to experimental and theoretical works from the literature using coarse-grained representations of poly(acrylic acid) (PAA) and poly(2-vinyl pyridine) (P2VP) polymer-based brushes. As the Born self-energy of ions can be straightforwardly included in the numerical approach, we also study its effect on the local charge regulation mechanism of the brush. We find that its effect becomes significant when the brush is dense and exposed to high salt concentrations. The numerical methodology is then applied (1) to the study of the kinetics of collapse/swelling of a P2VP brush and (2) to the ability of an applied voltage to induce collapse/swelling of a PAA brush in a pH range close to the pK value of the polymer.
We investigate the morphologies of
block copolymers confined in the region between two concentric and
charged cylinders. The relative stability of a concentric lamellar
phase compared to one where the lamellae are oriented in the radial
direction is determined from the competition between long-range elastic
and electrostatic forces. We find in weak and strong segregation and
by single-chain-in-mean-field simulations that under sufficiently
strong voltage difference there is a phase transition from concentric
to radial lamellae containing defects. Above a threshold voltage the
block copolymer melt develops an interfacial instability at a finite
wavelength.
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