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.
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. In combination with recent work, this suggests that other, higher order molecular polybromide ions might be isolated.
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.
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; 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 a 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 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 Parsons-Lee correction.arXiv:1408.1199v1 [cond-mat.soft] 6 Aug 2014 2
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.
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