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Virtual Photon Pulse Characterisation using Machine Learning methods
No full textThe use of fast computational tools is important in the operation of X-ray free electron lasers, in order to predict the output of diagnostics when they are either destructive or unavailable. Physics-based simulations can be computationally intensive to provide estimates on a real-time basis. This proposed work explores the use of machine learning to provide operators with estimates of key photon pulse characteristics related to beam pointing. A data pipeline is set up and the method is applied to the SASE1 undulator line at the European XFEL. This case study evaluates the performance of the model for different amounts of training data
Fragmentation dynamics of CS2 dications and trications following S 2p ionization
No full textWe present the results from a detailed study of the fragmentation dynamics of and, formed in intense femtosecond soft x-ray pulses above the sulfur 2p edge, primarily through single core photoionization from the S 2p site, and subsequent Auger–Meitner decay(s). By combining three-dimensional velocity map imaging with covariance analysis, we determine the relative momenta of the ions produced in each two- and three-body fragmentation channel, at significantly higher ion count rates than conventional coincidence measurements. We shed new light on the wide range of fragmentation channels observed from the CS2 dication and trication, including channels that involve ionization-induced bond formation and fragmentations producing undetected neutral cofragments. In the latter case, a “native frames” approach is used to isolate contributions from concerted and sequential fragmentations and extract dynamical information about each step of a concerted fragmentation process. While dications often fragment sequentially, the trication is dominated by concerted fragmentation. The main trication fragmentation channel into S+ + C+ + S+ can be well-approximated by classical Coulombic simulations of the ground-state geometry distribution, reflecting both the nature of the trication potential energy surface and the rapid multiple ionization prior to substantial structural dynamics. This study demonstrates ways in which fundamental insights into the fragmentation dynamics of polycations following x-ray ionization may be extracted, which will be beneficial to future studies that employ time-resolved x-ray Coulomb explosion imaging to study ultrafast photochemistry
Extremely low stress and faceted nature of type II twinning in Ni-Mn-Ga shape memory alloys
No full textThe origin of extraordinarily low twinning stresses, at the level of 0.02 MPa, for type II twin boundaries in Ni-Mn-Ga single crystals has been a matter of discussion for at least three decades. In this sense, the atomic structure ofthis boundary has aroused great interest since it may provide a definitive answer related to extremely lowtwinning stress, practically no temperature dependence, irrational twinning plane, and a high migration rate.This points to fundamentally different dynamics of type II boundaries compared to other twin interconnections.For this reason, its irrational twin-plane character was supposed to decompose into arrays of facets with rationalcomponents relaxed by an arrangement of equally spaced disconnections. However, up to now, no one present aclear experimental evidence. This work shows that the macroscopic irrational character of the type II twinboundary is represented by two faceted rational components at the atomistic scale. Complementary, adislocation-free mechanism for easy twin boundary motion, including shuffle of atomic layers due to extremelysoft elastic response along the [110] direction, is proposed. The present model explains very weak or practicallynonexistent temperature sensitivity of twinning stress. The given concept enables breakthrough in technologicalapplications for a broad class of functional materials, including ferroelectrics and multiferroics, exhibiting almostzero lattice friction down to 1.7 K
pygid: a Python package for fast data reduction in grazing-incidence diffraction
No full textAdvances in X-ray and neutron sources, as well as in area-detector technologies, enable the recording of several terabytes of raw two-dimensional detector data in a single experiment. While several efficient integration and conversion tools are available for data collected in transmission geometry, analogous solutions for grazing-incidence diffraction (including grazing-incidence X-ray diffraction and grazing-incidence wide-angle X-ray scattering) experiments have not yet achieved the same level of efficiency. The development of new data analysis tools, including machine-learning-based software for X-ray data, necessitates the establishment of a standardized format for the converted data. To address these challenges, we have developed a new Python library, pygid, which is designed to facilitate fast data processing while providing compatibility with various raw data formats, a standardized data storage format and an intuitive interface for straightforward use. pygid supports three types of coordinate systems and both transmission and grazing-incidence geometries. It is capable of handling large datasets, performing one-dimensional line cuts and simulating expected Bragg peak positions for given structures. The package facilitates sample and experimental metadata curation in accordance with the FAIR principles. As an integral part of the broader mlgid pipeline, pygid serves as the initial step linking raw scattering patterns with machine learning tools for data analysis. The pygid package is accessible at https://github.com/mlgid-project
Surface structure of long-chain ionic liquids: Temperature and chain-length evolution
No full text: The surface-parallel depth-decaying layering at the room-temperature ionic liquid (RTIL)/air interface should exhibit a thermal behavior different from bulk’s locally-layered structure. The absence of an (attractive) upper-half-space of matter above the surface should compress the layer spacing and provide for a larger thermal variation compared to the bulk. At the same time, the flat and sharp liquid surface is expected to align the layers macroscopically, and thus enhance the layering depth beyond the range of the bulk’s local layering.: Temperature ( )-dependent X-ray reflectivity (XRR) measurements off the free surfaces of a homologous series of model RTILs [Cmim][NTf2] (C,even = 12 − 18, where is the carbon number of the cationic hydrocarbon chain). Such combined (, ) surface structure evolution is not currently available for any aprotic homologous RTIL series.: The surface layering exhibits an anomalous thermal contraction, as does the bulk, rather than a conventional expansion, with surface layer spacings falling below those of the bulk by 5-25%, and exhibiting larger contraction-increases with increasing . A 10-35% increase in the spacing-normalized layering range was also found at the surface compared to the bulk for all . Surprisingly, a hardening of the surface layers against -variations is found for increasing , shown by the decrease of the surface spacing’s thermal slope |( )∕ | with increasing , while the bulk softens, with its |( )∕ | increasing with . These bulk/surfacedifferences originate in the effects hypothesized above
Molecular identifiers of the evolutionarily conserved titin pseudokinase
No full textTitin kinase (TK) is an enigmatic pseudokinase specific to the striated muscle of vertebrates. Embedded within the contractile sarcomere and flanked by extensible regulatory tails, TK is thought to act as a mechanoreceptor that senses mechanical signals arising from muscle function. Studies on TK so far have focused narrowly on the human representative, whose phosphotransfer activity remains questioned. To investigate whether the pseudokinase character is a hallmark of TK, we studied sequences of distantly evolved fish representatives and rationalized conservation patterns by solving the crystal structure of TK from medaka (isoform b). We find that sequence deviations in functional motifs involved in ATP and magnesium binding, respectively θxK (θ: bulky hydrophobic residue) and EFG, are evolutionarily conserved in TK. Beyond the kinase domain, N- and C-terminal flanking tails show remarkable structural similarity across orthologues, even though sequence conservation is limited to individual residues and short motifs: a YD-motif in the N-terminal tail; a [R/K]H[R/K]RYY sequence, a R-7x-R motif and position -2 of the latter in the C-terminal tail. Motifs in the C-terminal tail consistently covary with the divergent functional motifs of TK, being part of its pseudokinase signature. Contrary with these general features, the putatively inhibitory interaction of the catalytic aspartate with a tyrosine from loop P+1 is primarily confined to mammals. Finally, based on sequence clustering analysis, we identify TK subgroupings and propose a classification of titin genes from fish into a and b isoforms (ttna and ttnb) that can assist future studies. A curated genomic annotation is provided