Morphological analysis of chiral rod clusters from a coarse-grained single-site chiral potential.

We present a coarse-grained single-site potential for simulating chiral interactions, with adjustable strength, handedness, and preferred twist angle. As an application, we perform basin-hopping global optimisation to predict the favoured geometries for clusters of chiral rods. The morphology phase diagram based upon these predictions has four distinct families, including previously reported structures for potentials that introduce chirality based on shape, such as membranes and helices. The transition between these two configurations reproduces some key features of experimental results for fd bacteriophage. The potential is computationally inexpensive, intuitive, and versatile; we expect it will be useful for large scale simulations of chiral molecules. For chiral particles confined in a cylindrical container we reproduce the behaviour observed for fusilli pasta in a jar. Hence this chiropole potential has the capability to provide insight into structures on both macroscopic and molecular length scales.

Dynamical properties of two- and three-dimensional colloidal clusters of six particles.

Colloidal clusters are important systems for studying self-assembly. Clusters of six colloidal particles attracting each other via short-ranged interactions have been recently studied both theoretically and experimentally. Here we present a computer modelling study of the thermodynamics and dynamics of these clusters using a short-ranged Morse potential in two and three dimensions. We combine energy landscape methods with comprehensive sampling, both of configurations using Markov chain Monte Carlo and also of trajectories using Langevin molecular dynamics propagation. We show that the interaction energies between the particles are probably greater than previously assumed. The rates predicted by transition state theory using harmonic vibrational densities of states are off by four orders of magnitude, since the effects of viscosity are not accounted for. In contrast, sampling short trajectories using an appropriate friction constant and discrete relaxation path sampling produces reasonable agreement with the experimental rates.