PyQCstrc.ico: a computing package for structural modelling of icosahedral quasicrystals.
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ABSTRACT:
SUBMITTER: Yamada T
PROVIDER: S-EPMC8366420 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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.
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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.
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