PyQCstrc.ico: a computing package for structural modelling of icosahedral quasicrystals.
Ontology highlight
ABSTRACT:
SUBMITTER: Yamada T
PROVIDER: S-EPMC8366420 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Quasicrystals (QCs), first discovered in 1984, generally do not exhibit long-range magnetic order. Here, we report on long-range magnetic order in the real icosahedral quasicrystals (i QCs) Au-Ga-Gd and Au-Ga-Tb. The Au65Ga20Gd15 i QC exhibits a ferromagnetic transition at TC = 23 K, manifested as a sharp anomaly in both magnetic susceptibility and specific heat measurements, along with an appearance of magnetic Bragg peak below TC. This is the first observation of long-range magnetic order in a real quasicrystal, in contrast to the spin-glass-like behaviors observed for the other magnetic quasicrystals found to date. Moreover, when Gd is replaced by Tb, i.e., for the Au65Ga20Tb15 i QC, a ferromagnetic behavior is still retained with TC = 16 K. Although the sharp anomaly in the specific heat observed for the Au65Ga20Gd15 i QC becomes broadened upon Tb substitution, neutron diffraction experiments clearly show marked development of magnetic Bragg peaks just below TC, indicating long-range magnetic order for the Au65Ga20Tb15 i QC also. Our findings can contribute to the further investigation of exotic magnetic orders formed on real quasiperiodic lattices with unprecedented highest global symmetry, i.e., icosahedral symmetry.
| S-EPMC8640986 | biostudies-literature
Project description:A systematic study of the structures of ternary icosahedral Yb–Cd–Mg quasicrystals with different Mg contents has been carried out by single-crystal X-ray diffraction; occupational and positional disorder in the resulting structures was compared with that in a Yb–Cd–Mg 1/1 approximant. Atomic structures of ternary icosahedral (i) Yb–Cd–Mg quasicrystals (QCs) with five different Mg contents up to 46.4?at.% and a corresponding 1/1 approximant (AP), which has a composition of Yb13.3Cd70.3Mg16.5, have been analysed by single-crystal X-ray diffraction. The structures of the iQCs were found to be isostructural to the parent i-YbCd5.7, which consists of a so-called Tsai-type rhombic triacontahedron (RTH) cluster and double Friauf polyhedron, and that of the 1/1 AP was found to be isostructural to YbCd6, which is described by a body-centred packing of the same type of RTH cluster. In the iQCs, it was found that there are three types of Cd/Mg occupation, namely, Cd preferential site, Mg preferential site and Cd/Mg mixed site, and the occupation probabilities of Mg atoms at the Mg preferential site show a saturation behaviour around the Mg content of 20?at.%. This selective Mg occupation is identified as a cause of the non-linear increase in the icosahedral lattice constant with increasing Mg content. The 1/1 AP has a similar selective Mg occupation to that of the iQCs in terms of the shell structures of the Tsai-type RTH cluster. In both iQCs and the 1/1 AP, the Mg preferential sites have a smaller number of Yb atoms among their coordination numbers. Moreover, short-range order (s.r.o.) diffuse scattering was observed on the diffraction patterns of the iQCs at the positions corresponding to a face-centred-type (F-type) icosahedral superlattice. The F-type s.r.o. was found to result from the Mg substitution.
| S-EPMC5744414 | biostudies-literature
Project description:Non-Fermi-liquid (NFL), a significant deviation from Fermi-liquid theory, usually emerges near an order-disorder phase transition at absolute zero. Recently, a diverging susceptibility toward zero temperature was observed in a quasicrystal (QC). Since an electronic long-range ordering is normally absent in QCs, this anomalous behaviour should be a new type of NFL. Here we study high-resolution partial-fluorescence-yield x-ray absorption spectroscopy on Yb-based intermediate-valence icosahedral QCs and cubic approximant crystals (ACs), some of which are new materials, to unveil the mechanism of the NFL. We find that for both forms of QCs and ACs, there is a critical lattice parameter where Yb-valence and magnetism concomitantly exhibit singularities, suggesting a critical-valence-fluctuation-induced NFL. The present result provides an intriguing structure-property relationship of matter; size of a Tsai-type cluster (that is a common local structure to both forms) tunes the NFL whereas translational symmetry (that is present in ACs but absent in QCs) determines the nature of the NFL against the external/chemical pressure.
| S-EPMC7553930 | biostudies-literature
Project description:The statistics of how the local environment of a particle looks like, e.g., given by the distribution of nearest neighbor distances or the sizes of Voronoi cells, is important as a starting point for the calculation of many material properties like electronic or photonic band structures. Here we study local environments that occur in quasicrystals with large rotational symmetry. Both with analytical considerations based on geometric arguments and with an analysis of a large number of numerically created patches of high-symmetry quasicrystals we find that the Voronoi area's distribution reaches a bimodal curve and that in the limit of large rotational symmetries the distribution of nearest neighbor distance converges against a universal curve, where [Formula: see text] of the vertices have their nearest neighbor at a normalized distance equal to 1, while for the other [Formula: see text] the nearest neighbor is at a distance less than 1. Therefore, the statistics of local environments is non-trivial but independent of the specific rotational symmetry. Thus properties that only depend on local environments are expected to be universal for all high-symmetry quasicrystals.
| S-EPMC10550988 | biostudies-literature
Project description:High-throughput measurements of DNA methylation are increasingly becoming a mainstay of biomedical investigations. While the methylation status of individual cytosines can sometimes be informative, several recent papers have shown that the functional role of DNA methylation is better captured by a quantitative analysis of the spatial variation of methylation across a genomic region.Here, we present BPRMeth, a Bioconductor package that quantifies methylation profiles by generalized linear model regression. The original implementation has been enhanced in two important ways: we introduced a fast, variational inference approach that enables the quantification of Bayesian posterior confidence measures on the model, and we adapted the method to use several observation models, making it suitable for a diverse range of platforms including single-cell analyses and methylation arrays.http://bioconductor.org/packages/BPRMeth.Supplementary data are available at Bioinformatics online.
| S-EPMC6041802 | biostudies-other
Project description:BackgroundIt is scientifically and ethically imperative that the results of statistical analysis of biomedical research data be computationally reproducible in the sense that the reported results can be easily recapitulated from the study data. Some statistical analyses are computationally a function of many data files, program files, and other details that are updated or corrected over time. In many applications, it is infeasible to manually maintain an accurate and complete record of all these details about a particular analysis.ResultsTherefore, we developed the rctrack package that automatically collects and archives read only copies of program files, data files, and other details needed to computationally reproduce an analysis.ConclusionsThe rctrack package uses the trace function to temporarily embed detail collection procedures into functions that read files, write files, or generate random numbers so that no special modifications of the primary R program are necessary. At the conclusion of the analysis, rctrack uses these details to automatically generate a read only archive of data files, program files, result files, and other details needed to recapitulate the analysis results. Information about this archive may be included as an appendix of a report generated by Sweave or knitR. Here, we describe the usage, implementation, and other features of the rctrack package. The rctrack package is freely available from http://www.stjuderesearch.org/site/depts/biostats/rctrack under the GPL license.
| S-EPMC4026591 | biostudies-literature
Project description:Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities.The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user-friendly r implementation.We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio-temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single-species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence-absence data.The package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with r.
| S-EPMC7074067 | biostudies-literature
Project description:Viruses have evolved protein containers with a wide spectrum of icosahedral architectures to protect their genetic material. The geometric constraints defining these container designs, and their implications for viral evolution, are open problems in virology. The principle of quasi-equivalence is currently used to predict virus architecture, but improved imaging techniques have revealed increasing numbers of viral outliers. We show that this theory is a special case of an overarching design principle for icosahedral, as well as octahedral, architectures that can be formulated in terms of the Archimedean lattices and their duals. These surface structures encompass different blueprints for capsids with the same number of structural proteins, as well as for capsid architectures formed from a combination of minor and major capsid proteins, and are recurrent within viral lineages. They also apply to other icosahedral structures in nature, and offer alternative designs for man-made materials and nanocontainers in bionanotechnology.
| S-EPMC6765026 | biostudies-literature
Project description:BackgroundSince more than a million single-nucleotide polymorphisms (SNPs) are analyzed in any given genome-wide association study (GWAS), performing multiple comparisons can be problematic. To cope with multiple-comparison problems in GWAS, haplotype-based algorithms were developed to correct for multiple comparisons at multiple SNP loci in linkage disequilibrium. A permutation test can also control problems inherent in multiple testing; however, both the calculation of exact probability and the execution of permutation tests are time-consuming. Faster methods for calculating exact probabilities and executing permutation tests are required.MethodsWe developed a set of computer programs for the parallel computation of accurate P-values in haplotype-based GWAS. Our program, ParaHaplo, is intended for workstation clusters using the Intel Message Passing Interface (MPI). We compared the performance of our algorithm to that of the regular permutation test on JPT and CHB of HapMap.ResultsParaHaplo can detect smaller differences between 2 populations than SNP-based GWAS. We also found that parallel-computing techniques made ParaHaplo 100-fold faster than a non-parallel version of the program.ConclusionParaHaplo is a useful tool in conducting haplotype-based GWAS. Since the data sizes of such projects continue to increase, the use of fast computations with parallel computing--such as that used in ParaHaplo--will become increasingly important. The executable binaries and program sources of ParaHaplo are available at the following address: http://sourceforge.jp/projects/parallelgwas/?_sl=1.
| S-EPMC2774321 | biostudies-literature
Project description:We investigate two-dimensional (2D) assembly of the icosahedral turnip yellow mosaic virus (TYMV) under cationic lipid monolayers at the aqueous solution–vapor interface. The 2D crystallization of TYMV has been achieved by enhancing electrostatically induced interfacial adsorption, an approach recently demonstrated for another virus. In situ X-ray scattering reveals two close-packed 2D crystalline phases of TYMV that are distinct from the previously reported hexagonal and centered square (?2 × ?2) arrays of TYMV. One of the newly observed phases arises from either a dimeric double-square (2 × 1) or tetrameric square (2 × 2) unit cell. The other is a rhombic crystal with a lattice angle of 80°. The two observed crystal phases are substantially less dense (by over 10%) than a 2D lattice of TYMV could be according to its known size and shape, indicating that local anisotropic interparticle interactions play a key role in stabilizing these crystals. TYMV's anisotropy attributes and numerical analysis of 2D arrays of virus-shaped particles are used to derive a model for the rhombic crystal in which the particle orientation is consistent with the electrostatic lipid–TYMV attraction and the interparticle contacts exhibit steric complementarity. The interplay between particle anisotropy and packing is contrasted between the rhombic crystal model and the square (?2 × ?2) crystal. This study highlights how the high symmetry and subtle asphericity of icosahedral particles enrich the variety and complexity of ordered 2D structures that can be generated through self-assembly.
| S-EPMC4828961 | biostudies-other