Enumeration of nonequivalent substitutional structures using advanced data structure of binary decision diagram.

A derivative structure is a nonequivalent substitutional atomic configuration derived from a given primitive cell. The enumeration of derivative structures plays an essential role in searching for the ground states in multicomponent systems. However, it is computationally difficult to enumerate derivative structures if the number of derivative structures of a target system becomes huge. In this study, we introduce a novel compact data structure of the zero-suppressed binary decision diagram (ZDD) for enumerating derivative structures much more efficiently. We show its simple applications to the enumeration of structures derived from the face-centered cubic and hexagonal close-packed lattices in binary, ternary, and quaternary systems. The present ZDD-based procedure should contribute to computational approaches based on derivative structures in physics and materials science.

Algorithm for spin symmetry operation search.

A spin space group provides a suitable way of fully exploiting the symmetry of a spin arrangement with a negligible spin-orbit coupling. There has been a growing interest in applying spin symmetry analysis with the spin space group in the field of magnetism. However, there is no established algorithm to search for spin symmetry operations of the spin space group. This paper presents an exhaustive algorithm for determining the spin symmetry operations of commensurate spin arrangements. The present algorithm searches for spin symmetry operations from the symmetry operations of a corresponding nonmagnetic crystal structure and determines their spin-rotation parts by solving a Procrustes problem. An implementation is distributed under a permissive free software license in spinspg Version 0.1.1, available at https://github.com/spglib/spinspg.

Algorithms for magnetic symmetry operation search and identification of magnetic space group from magnetic crystal structure.

A crystal symmetry search is crucial for computational crystallography and materials science. Although algorithms and implementations for the crystal symmetry search have been developed, their extension to magnetic space groups (MSGs) remains limited. In this paper, algorithms for determining magnetic symmetry operations of magnetic crystal structures, identifying magnetic space-group types of given MSGs, searching for transformations to a Belov-Neronova-Smirnova (BNS) setting, and symmetrizing the magnetic crystal structures using the MSGs are presented. The determination of magnetic symmetry operations is numerically stable and is implemented with minimal modifications from the existing crystal symmetry search. Magnetic space-group types and transformations to the BNS setting are identified by a two-step approach combining space-group-type identification and the use of affine normalizers. Point coordinates and magnetic moments of the magnetic crystal structures are symmetrized by projection operators for the MSGs. An implementation is distributed with a permissive free software license in spglib v2.0.2: https://github.com/spglib/spglib.

High-throughput single-base mismatch detection for genotyping of UDP-glucuronosyltransferase (UGT1A1) with probe capture assay coupled with modified allele-specific primer extension reaction (MASPER).

We have developed a new method based on specific primer extension reactions coupled with plate hybridization for high-throughput genotyping of single-base mutations. To improve the switching characteristics of the primer extension reaction, we introduced an artificial mismatch two bases upstream of the 3'-terminal base in the detection primers. A set of primers that correspond to wild-type and mutant DNA segments can be used to accurately analyze single-base mutations. The termini of these primers are at the mutation positions. The primer extension products produced by polymerase chain reaction (PCR) were captured by an oligonucleotide probe immobilized on the surface of microtiter wells and were detected by a colorimetric assay using the streptavidin-conjugated horseradish peroxidase. We used the new method to genotype 96 individuals for 211G>A (G71R) and 119 for 1456T>G (Y486D) in the UDP-glucuronosyltransferase1A1 gene; the results were completely concordant with those found by direct sequencing. The proposed method includes ordinary PCR and a microplate assay format, and may be used in routine laboratory tests.