Evolution of Mn1-xGexBi2Te4 Electronic Structure under Variation of Ge Content.

One of the approaches to manipulate MnBi2Te4 properties is the magnetic dilution, which inevitably affects the interplay of magnetism and band topology in the system. In this work, we carried out angle-resolved photoemission spectroscopy (ARPES) measurements and density functional theory (DFT) calculations for analysing changes in the electronic structure of Mn1-xGexBi2Te4 that occur under parameter x variation. We consider two ways of Mn/Ge substitution: (i) bulk doping of the whole system; (ii) surface doping of the first septuple layer. For the case (i), the experimental results reveal a decrease in the value of the bulk band gap, which should be reversed by an increase when the Ge concentration reaches a certain value. Ab-initio calculations show that at Ge concentrations above 50%, there is an absence of the bulk band inversion of the Te pz and Bi pz contributions at the Γ-point with significant spatial redistribution of the states at the band gap edges into the bulk, suggesting topological phase transition in the system. For case (ii) of the vertical heterostructure Mn1-xGexBi2Te4/MnBi2Te4, it was shown that an increase of Ge concentration in the first septuple layer leads to effective modulation of the Dirac gap in the absence of significant topological surface states of spatial redistribution. The results obtained indicate that surface doping compares favorably compared to bulk doping as a method for the Dirac gap value modulation.

Sublattice Ferrimagnetism in Quasifreestanding Graphene.

We show that graphene can be magnetized by coupling to a ferromagnetic Co film through a Au monolayer. The presence of dislocation loops under graphene leads to a ferrimagnetic ordering of moments in the two C sublattices. It is shown that the band gap of ∼80 meV in the K[over ¯] point has a magnetic nature and exists for ferrimagnetic ordering. Interplay between Rashba and exchange couplings is evidenced by spin splitting asymmetry in spin-ARPES measurements and fully supported by DFT calculation of a (9×9) unit cell. Owing to sign-opposite Berry curvatures for K[over ¯] and K[over ¯]^{'} valleys, the synthesized system is promising for the realization of a circular dichroism Hall effect.

Estimating the Orientation of 4f Magnetic Moments by Classical Photoemission.

To use efficiently the magnetic functionalities emerging at the surfaces or interfaces of novel lanthanides-based materials, there is a need for complementary methods to probe the atomic-layer resolved magnetic properties. Here, we show that 4f photoelectron spectroscopy is highly sensitive to the collective orientation of 4f magnetic moments and, thus, a powerful tool for characterizing the related properties. To demonstrate this, we present the results of systematic study of a family of layered crystalline 4f-materials, which are crystallized in the body-centered tetragonal ThCr2Si2 structure. Analysis of 4f spectra indicates that the 4f moments at the surface experience a strong reorientation with respect to the bulk, caused by changes of the crystal-electric field. The presented database of the computed 4f spectra for all trivalent rare-earth ions in their different MJ states will facilitate the estimation of the orientation of the 4f magnetic moments in the layered 4f-systems for efficient control of their magnetic properties.

Direct Spectroscopic Evidence of Magnetic Proximity Effect in MoS2 Monolayer on Graphene/Co.

A magnetic field modifies optical properties and provides valley splitting in a molybdenum disulfide (MoS2) monolayer. Here we demonstrate a scalable approach to the epitaxial synthesis of MoS2 monolayer on a magnetic graphene/Co system. Using spin- and angle-resolved photoemission spectroscopy we observe a magnetic proximity effect that causes a 20 meV spin-splitting at the Γ̅ point and canting of spins at the K̅ point in the valence band toward the in-plane direction of cobalt magnetization. Our density functional theory calculations reveal that the in-plane spin component at K̅ is localized on Co atoms in the valence band, while in the conduction band it is localized on the MoS2 layer. The calculations also predict a 16 meV spin-splitting at the Γ̅ point and 8 meV K̅-K'¯ valley asymmetry for an out-of-plane magnetization. These findings suggest control over optical transitions in MoS2 via Co magnetization. Our estimations show that the magnetic proximity effect is equivalent to the action of the magnetic field as large as 100 T.

IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction.

We describe fast and accurate algorithm for IonTorrent read error correction capable of significantly reducing the number of sequencing errors over the wide range of data sets. IonHammer is implemented in C++ and is freely available as part of the SPAdes genome assembler package.

Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity.

When analyzing mass spectrometry imaging data sets, assigning a molecule to each of the thousands of generated images is a very complex task. Recent efforts have taken lessons from (tandem) mass spectrometry proteomics and applied them to imaging mass spectrometry metabolomics, with good results. Our goal is to go a step further in this direction and apply a well established, data-driven method to improve the results obtained from an annotation engine. By using a data-driven rescoring strategy, we are able to consistently improve the sensitivity of the annotation engine while maintaining control of statistics like estimated rate of false discoveries. All the code necessary to run a search and extract the additional features can be found at https://github.com/anasilviacs/sm-engine and to rescore the results from a search in https://github.com/anasilviacs/rescore-metabolites .

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.

High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM). We introduce a metabolite-signal match score and a target-decoy FDR estimate for spatial metabolomics.

Sambamba: fast processing of NGS alignment formats.

UNLABELLED: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. Sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability. AVAILABILITY AND IMPLEMENTATION: Sambamba is free and open source software, available under a GPLv2 license. Sambamba can be downloaded and installed from http://www.open-bio.org/wiki/Sambamba.Sambamba v0.5.0 was released with doi:10.5281/zenodo.13200.