A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures

[Background]Measuring similarities between tree structured data is important for analysis of RNA secondary structures, phylogenetic trees, glycan structures, and vascular trees. The edit distance is one of the most widely used measures for comparison of tree structured data. However, it is known that computation of the edit distance for rooted unordered trees is NP-hard. Furthermore, there is almost no available software tool that can compute the exact edit distance for unordered trees. [Results]In this paper, we present a practical method for computing the edit distance between rooted unordered trees. In this method, the edit distance problem for unordered trees is transformed into the maximum clique problem and then efficient solvers for the maximum clique problem are applied. We applied the proposed method to similar structure search for glycan structures. The result suggests that our proposed method can efficiently compute the edit distance for moderate size unordered trees. It also suggests that the proposed method has the accuracy comparative to those by the edit distance for ordered trees and by an existing method for glycan search. [Conclusions]The proposed method is simple but useful for computation of the edit distance between unordered trees. The object code is available upon request

Fundamental physics activities with pulsed neutron at J-PARC(BL05)

"Neutron Optics and Physics (NOP/ BL05)" at MLF in J-PARC is a beamline for studies of fundamental physics. The beamline is divided into three branches so that different experiments can be performed in parallel. These beam branches are being used to develop a variety of new projects. We are developing an experimental project to measure the neutron lifetime with total uncertainty of 1 s (0.1%). The neutron lifetime is an important parameter in elementary particle and astrophysics. Thus far, the neutron lifetime has been measured by several groups; however, different values are obtained from different measurement methods. This experiment is using a method with different sources of systematic uncertainty than measurements conducted to date. We are also developing a source of pulsed ultra-cold neutrons (UCNs) produced from a Doppler shifter are available at the unpolarized beam branch. We are developing a time focusing device for UCNs, a so called "rebuncher", which can increase UCN density from a pulsed UCN source. At the low divergence beam branch, an experiment to search an unknown intermediate force with nanometer range is performed by measuring the angular dependence of neutron scattering by noble gases. Finally the beamline is also used for the research and development of optical elements and detectors. For example, a position sensitive neutron detector that uses emulsion to achieve sub-micrometer resolution is currently under development. We have succeeded in detecting cold and ultra-cold neutrons using the emulsion detector.Comment: 9 pages, 5 figures, Proceedings of International Conference on Neutron Optics (NOP2017

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin

X線自由電子レーザーを用いて、光照射によるチャネルロドプシンの構造変化の過程を捉えることに成功. 京都大学プレスリリース. 2021-03-26.Channelrhodopsins (ChRs) are microbial light-gated ion channels utilized in optogenetics to control neural activity with light . Light absorption causes retinal chromophore isomerization and subsequent protein conformational changes visualized as optically distinguished intermediates, coupled with channel opening and closing. However, the detailed molecular events underlying channel gating remain unknown. We performed time-resolved serial femtosecond crystallographic analyses of ChR by using an X-ray free electron laser, which revealed conformational changes following photoactivation. The isomerized retinal adopts a twisted conformation and shifts toward the putative internal proton donor residues, consequently inducing an outward shift of TM3, as well as a local deformation in TM7. These early conformational changes in the pore-forming helices should be the triggers that lead to opening of the ion conducting pore

A clique-based method using dynamic programming for computing edit distance between unordered trees.

Abstract Many kinds of tree-structured data, such as RNA secondary structures, have become available due to the progress of techniques in the field of molecular biology. To analyze the tree-structured data, various measures for computing the similarity between them have been developed and applied. Among them, tree edit distance is one of the most widely used measures. However, the tree edit distance problem for unordered trees is NP-hard. Therefore, it is required to develop efficient algorithms for the problem. Recently, a practical method called clique-based algorithm has been proposed, but it is not fast for large trees. This article presents an improved clique-based method for the tree edit distance problem for unordered trees. The improved method is obtained by introducing a dynamic programming scheme and heuristic techniques to the previous clique-based method. To evaluate the efficiency of the improved method, we applied the method to comparison of real tree structured data such as glycan structures. For large tree-structures, the improved method is much faster than the previous method. In particular, for hard instances, the improved method achieved more than 100 times speed-up