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Under pressure, metals exhibit increasingly shorter interatomic distances. Intuitively, this response is expected to be accompanied by an increase in the widths of the valence and conduction bands and hence a more pronounced free-electron-like behaviour. But at the densities that can now be achieved experimentally, compression can be so substantial that(More)
a r t i c l e i n f o a b s t r a c t Evolutionary crystal structure prediction proved to be a powerful approach in discovering new materials. Certain limitations are encountered for systems with a large number of degrees of freedom (" large systems ") and complex energy landscapes (" complex systems "). We explore the nature of these limitations and(More)
Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary(More)
Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have(More)
We explore whether the topology of energy landscapes in chemical systems obeys any rules and what these rules are. To answer this and related questions we use several tools: (i) Reduced energy surface and its density of states, (ii) descriptor of structure called fingerprint function, which can be represented as a one-dimensional function or a vector in(More)
Prediction of the stable crystal structure on the basis of only the chemical composition is one of the central problems of condensed matter physics, which for a long time remained unsolved. The recently developed evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography) made an important progress in this field, enabling(More)
USPEX is a crystal structure predictor based on an evolutionary algorithm. Every USPEX run produces hundreds or thousands of crystal structures, some of which may be identical. To ease the extraction of unique and potentially interesting structures we applied usual high-dimensional classification concepts to the unusual field of crystallography. We(More)
Prediction of stable crystal structures at given pressure-temperature conditions, based only on the knowledge of the chemical composition, is a central problem of condensed matter physics. This extremely challenging problem is often termed “crystal structure prediction problem,” and recently developed evolutionary algorithm USPEX (Universal Structure(More)
MOTIVATION The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our(More)
To support CSCS research users we built STM3, a software platform on which advanced chemistry visualization techniques can be integrated. Its main goal is not to replace existing tools, but to provide functionalities not covered by them. STM3’s unusual characteristic among chemistry visualization tools is its ability to combine chemistry and general(More)