Self-assembly behaviour of hetero-nuclear Janus dumbbells.

We investigate the fluid structure and self-assembly of a system of Janus dumbbells by means of aggregation-volume-bias Monte Carlo simulations and Simulated Annealing techniques. In our approach, Janus dumbbells model asymmetric colloidal particles constituted by two tangent (touching) spheres (labelled as h and s) of different sizes and interaction properties: specifically, the h spheres interact with all other spheres belonging to different dumbbells via hard-sphere potentials, whereas two s spheres interact via a square-well potential. By introducing a parameter α ∈ [0,2] that controls the size ratio between the h and s spheres, we are able to investigate the overall phase behaviour of Janus dumbbells as a function of α. In a previous paper (O'Toole et al., Soft Matter, 2017, 13, 803) we focused on the region where the s sphere is larger than the h sphere (α > 1), documenting the presence of a variety of phase behaviours. Here we investigate a different regime of size ratios, predominantly where the hard sphere is larger than (or comparable to) the attractive one. Under these conditions, we observe the onset of many different self-assembled super-structures. Depending on the specific value of α we document the presence of spherical clusters (micelles) progressively evolving into more exotic structures including platelets, filaments, networks and percolating fluids, sponge structures and lamellar phases. We find no evidence of a gas-liquid phase separation for α ≤ 1.1, since under these conditions it is pre-empted by the development of self-assembled phases.

Phase separation and self-assembly of colloidal dimers with tunable attractive strength: from symmetrical square-wells to Janus dumbbells.

We numerically investigate colloidal dimers with asymmetric interaction strengths to study how the interplay between molecular geometry, excluded volume effects and attractive forces determines the overall phase behavior of such systems. Specifically, our model is constituted by two rigidly-connected tangent hard spheres interacting with other particles in the first instance via identical square-well attractions. Then, one of the square-well interactions is progressively weakened, until only the corresponding bare hard-core repulsion survives, giving rise to a "Janus dumbbell" model. We investigate structure, thermodynamics and phase behavior of the model by means of successive umbrella sampling and Monte Carlo simulations. In most of the cases, the system behaves as a standard simple fluid, characterized by a gas-liquid phase separation, for sufficiently low temperatures. In these conditions we observe a remarkable linear scaling of the critical temperature as a function of the interaction strength. But, as the interaction potential approaches the Janus dumbbell limit, we observe the spontaneous formation of self-assembled lamellar structures, preempting the gas-liquid phase separation. Comparison with previous studies allows us to pinpoint the role of the interaction range in controlling the onset of ordered structures and the competition between the formation of these structures and gas-liquid condensation.

Self-assembly of hard helices: a rich and unconventional polymorphism.

Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit, from natural polynucleotides and polypeptides to synthetic helical polymers, and from bacterial flagella to colloidal helices. Here we present an extensive investigation of the phase diagram of hard helices using a variety of methods. Isobaric Monte Carlo numerical simulations are used to trace the phase diagram; on going from the low-density isotropic to the high-density compact phases a rich polymorphism is observed, exhibiting a special chiral screw-like nematic phase and a number of chiral and/or polar smectic phases. We present full characterization of the latter, showing that they have unconventional features, ascribable to the helical shape of the constituent particles. Equal area construction is used to locate the isotropic-to-nematic phase transition, and the results are compared with those stemming from an Onsager-like theory. Density functional theory is also used to study the nematic-to-screw-nematic phase transition; within the simplifying assumption of perfectly parallel helices, we compare different levels of approximation, that is second- and third-virial expansions and a Parsons-Lee correction.

Communication: from rods to helices: evidence of a screw-like nematic phase.

Evidence of a special chiral nematic phase is provided using numerical simulation and Onsager theory for systems of hard helical particles. This phase appears at the high density end of the nematic phase, when helices are well aligned, and is characterized by the C2 symmetry axes of the helices spiraling around the nematic director with periodicity equal to the particle pitch. This coupling between translational and rotational degrees of freedom allows a more efficient packing and hence an increase of translational entropy. Suitable order parameters and correlation functions are introduced to identify this screw-like phase, whose main features are then studied as a function of radius and pitch of the helical particles. Our study highlights the physical mechanism underlying a similar ordering observed in colloidal helical flagella [E. Barry, Z. Hensel, Z. Dogic, M. Shribak, and R. Oldenbourg, Phys. Rev. Lett. 96, 018305 (2006)] and raises the question of whether it could be observed in other helical particle systems, such as DNA, at sufficiently high densities.

Crystallization of the Lewis-Wahnström ortho-terphenyl model.

Crystallization is observed during microsecond long molecular dynamics simulations of bent trimers, a molecular model proposed by Lewis and Wahnström for ortho-terphenyl. In the crystal, the three spheres that make up the rigid molecule sit near sites of a body centered cubic lattice. The trimer bond angle is almost optimal for this structure. The crystal exhibits orientational disorder with the molecules aligned randomly along the three Cartesian axis, i.e., cubatic orientational order. The rotational and translational mobilities exhibit only modest decreases on crystallization, by factors of 10 and 3, respectively. The rotational relaxation does change from Debye-like in the liquid to large angle jumps in the crystal. We consider the origin of the superior glass forming ability of the trimer over the monatomic liquid.

Wikidata as a knowledge graph for the life sciences.

Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.

The densest packing of AB binary hard-sphere homogeneous compounds across all size ratios.

This paper considers the homogeneous packing of binary hard spheres in an equimolar stoichiometry, and postulates the densest packing at each sphere size ratio. Monte Carlo simulated annealing optimizations are seeded with all known atomic inorganic crystal structures, and the search is performed within the degrees of freedom associated with each homogeneous AB structure type. Structures isopointal to the FeB structure type are found to have the highest packing fraction at all sphere size ratios. The optimized structures match or improve on the best previously demonstrated packings of this type, and show that compound structures can pack more densely than segregated close-packed structures at all radius ratios less than 0.62.

Structural searches using isopointal sets as generators: densest packings for binary hard sphere mixtures.

Algorithms to search for crystal structures that optimize some extensive property (energy, volume, etc) typically make use of random particle reorganizations in the context of one or more numerical techniques such as simulated annealing, genetic algorithms or biased random walks, applied to the coordinates of every particle in the unit cell, together with the cell angles and lengths. In this paper we describe the restriction of such searches to predefined isopointal sets, breaking the problem into countable sub-problems which exploit crystal symmetries to reduce the dimensionality of the search space. Applying this method to the search for maximally packed mixtures of hard spheres of two sizes, we demonstrate that the densest packed structures can be identified by searches within a couple of isopointal sets. For the A(2)B system, the densest known packings over the entire tested range 0.2 < r(A)/r(B) < 2.5, including some improvements on previous optima, can all be identified by searches within a single isopointal set. In the case of the AB composition, searches of two isopointal sets generate the densest packed structures over the radius ratio range 0.2 < r(A)/r(B) < 5.0.