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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 {it{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.
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DN
Dynamics of a coarse-grained model for the room-temperature ionic liquid, 1-ethyl-3-methylimidazolium hexafluorophosphate, couched in the united-atom site representation are studied via molecular dynamics simulations. The dynamically heterogeneous be
Asymmetrically charged, nonspherical colloidal particles in general perform complex rotations and oblique motions under an electric field. The interplay of electrostatic and hydrodynamic forces complicate the prediction of these motions. We demonstra
Melts of 3-dimensional dendritic beads-springs, namely coarse-grained soft-clusters, are studied by molecular dynamics simulations. The goal is to elucidate the unique dynamics of giant molecules, or generally speaking, 3-dimensional architectured po
The fractal properties of the total potential energy V as a function of time t are studied for a number of systems, including realistic models of proteins (PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the exponent gamma,