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.

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.

The stabilization of tubular crystals in mixtures of spherical particles.

Novel crystal structures in binary atomic mixtures arise when the attractive well is wide enough to allow double occupancy by small particles. The resulting crystals consist of ordered packings of self assembled linear structures comprised of a cylindrical tube of large particles enclosing a close packed core of small particles that corresponds to a stacking of overlapping icosahedra. We show that the stability of these structures depends on two essential features of the spherically symmetric pairwise interactions: (i) a radius ratio between 0.

Phase diagram of heteronuclear Janus dumbbells.

Using aggregation-volume-bias Monte Carlo simulations along with successive umbrella sampling and histogram re-weighting, we study the phase diagram of a system of dumbbells formed by two touching spheres having variable sizes, as well as different interaction properties. The first sphere (h) interacts with all other spheres belonging to different dumbbells with a hard-sphere potential. The second sphere (s) interacts via a square-well interaction with other s spheres belonging to different dumbbells and with a hard-sphere potential with all remaining h spheres.

Density and glass forming ability in amorphous atomic alloys: The role of the particle softness.

A key property of glass forming alloys, the anomalously small volume difference with respect to the crystal, is shown to arise as a direct consequence of the soft repulsive potentials between metals. This feature of the inter-atomic potential is demonstrated to be responsible for a significant component of the glass forming ability of alloys due to the decrease in the enthalpy of fusion and the associated depression of the freezing point.

Long range stress correlations in the inherent structures of liquids at rest.

Simulation studies of the atomic shear stress in the local potential energy minima (inherent structures) are reported for binary liquid mixtures in 2D and 3D. These inherent structure stresses are fundamental to slow stress relaxation and high viscosity in supercooled liquids. We find that the atomic shear stress in the inherent structures (IS's) of both liquids at rest exhibits slowly decaying anisotropic correlations.

Telephone Transmission and Earwitnesses: Performance on Voice Parades Controlled for Voice Similarity.

The effect of telephone transmission on a listener's ability to recognise a speaker in a voice parade is investigated. A hundred listeners (25 per condition) heard 1 of 5 'target' voices, then returned a week later for a voice parade. The 4 conditions were: target exposure and parade both at studio quality; exposure and parade both at telephone quality; studio exposure with telephone parade, and vice versa.

The formation of high-order polybromides in a room-temperature ionic liquid: from monoanions ([Br5 ](-) to [Br11 ](-) ) to the isolation of [PC16 H36 ]2 [Br24 ] as determined by van der Waals Bonding Radii.

An unprecedented diversity of high-order bromine catenates (anionic polybromides) was generated in a tetraalkylphosphonium-based room temperature ionic liquid system. Raman spectroscopy was used to identify polybromide monoanions ranging from [Br5 ](-) to [Br11 ](-) in the bulk solution, while single-crystal X-ray diffraction identified extended networks of linked [Br11 ](-) units, forming a previously unknown polymeric [Br24 ](2-) dianion. This represents the largest polybromide species identified to date.

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.

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.

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.

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.

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 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.