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In situ transmission electron microscopy as a toolbox for the emerging science of nanometallurgy
The paper describes a novel lab-on-a-chip approach that allows the observation of live nanoalloying and heat treatment at the nanoscale.
Expanding the Zinc Precursor Toolbox: A Comparative Study of Precursors for Thermal ALD of ZnO Thin Films
Atomic layer deposition (ALD) of zinc oxide (ZnO) has been widely researched using diethyl zinc (DEZ)-based methods. The significant importance of thin films of ZnO as transparent conductive oxides (TCO) in optoelectronic devices and photovoltaics warrants examining alternative Zn precursors for ZnO ALD as potential replacements for the pyrophoric DEZ. In this study, we investigated three alternative Zn precursors: Zn(EEKI)2, Zn(DMP)2, ZnEt(HMDS), in the process development for high-quality ZnO thin films and compared them to DEZ. The ALD processes were studied using in situ spectroscopic ellipsometry. The properties of the ALD ZnO films were characterized using ex situ X-ray photoelectron spectroscopy (XPS), Rutherford backscattering spectrometry and nuclear reaction analysis (RBS/NRA), X-ray diffraction (XRD), atomic force microscopy (AFM), transmission electron microscopy (TEM), and ultraviolet-visible (UV/Vis) spectrophotometry. These measurements confirmed the formation of pure, stoichiometric, and polycrystalline ZnO films using all four Zn precursors. Although the selected precursors are chemically diverse Zn compounds, they all yielded saturating ALD processes and high-quality ZnO thin films at 200 °C. This study highlights the potential benefits of alternative zinc precursors in designing ALD processes for ZnO thin films.
Towards a Portable Open-Source Tomography Toolbox: Containerizing Tomography Software with Docker
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Resonant ultrasound spectroscopy: The essential toolbox
Resonant Ultrasound Spectroscopy (RUS) is an ultrasound-based minimal-effort high-accuracy elastic modulus measurement technique. RUS as described here uses the mechanical resonances (normal modes of vibration or just modes) of rectangular parallelepiped or cylindrical specimens with a dimension of from a fraction of a millimeter to as large as will fit into the apparatus. Provided here is all that is needed so that the reader can construct and use a state-of-the-art RUS system. Included are links to open-source circuit diagrams, links to download Los Alamos National Laboratory open-source data acquisition software, links to request free analysis software, procedures for acquiring measurements, considerations on building transducers, 3-D printed stage designs, and a full mathematical explanation of how the analysis software extracts elastic moduli from resonances.
SCIP: a single-cell image processor toolbox
Abstract Summary Each cell is a phenotypically unique individual that is influenced by internal and external processes, operating in parallel. To characterize the dynamics of cellular processes one needs to observe many individual cells from multiple points of view and over time, so as to identify commonalities and variability. With this aim, we engineered a software, ‘SCIP’, to analyze multi-modal, multi-process, time-lapse microscopy morphological and functional images. SCIP is capable of automatic and/or manually corrected segmentation of cells and lineages, automatic alignment of different microscopy channels, as well as detect, count and characterize fluorescent spots (such as RNA tagged by MS2-GFP), nucleoids, Z rings, Min system, inclusion bodies, undefined structures, etc. The results can be exported into *mat files and all results can be jointly analyzed, to allow studying not only each feature and process individually, but also find potential relationships. While we exemplify its use on Escherichia coli, many of its functionalities are expected to be of use in analyzing other prokaryotes and eukaryotic cells as well. We expect SCIP to facilitate the finding of relationships between cellular processes, from small-scale (e.g. gene expression) to large-scale (e.g. cell division), in single cells and cell lineages. Availability and implementation http://www.ca3-uninova.org/project_scip Supplementary information Supplementary data are available at Bioinformatics online.
A selection function toolbox for subsets of astronomical catalogues
ABSTRACT Large catalogues are ubiquitous throughout astronomy, but most scientific analyses are carried out on smaller samples selected from these catalogues by chosen cuts on catalogued quantities. The selection function of that scientific sample – the probability that a star in the catalogue will satisfy these cuts and so make it into the sample – is thus unique to each scientific analysis. We have created a general framework that can flexibly estimate the selection function of a sample drawn from a catalogue in terms of position, magnitude and colour. Our method is unique in using the binomial likelihood and accounting for correlations in the selection function across position, magnitude, and colour using Gaussian processes and spherical harmonics. We have created a new open-source python package selectionfunctiontoolbox that implements this framework and used it to make three different estimates of the APOGEE DR16 red giant sample selection function, as a subset of 2MASS, with each estimate using an increasing amount of technical knowledge of the APOGEE targeting. In a companion paper, we applied our methodology to derive estimates of the astrometric and spectroscopic selection functions of Gaia EDR3. Our framework will make it trivial for astrophysicists to estimate the selection function that they should be using with the custom sample of stars that they have chosen to answer their scientific question.
Enriching the Quantum Toolbox of Ultracold Molecules with Rydberg Atoms
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MoChlo: A Versatile, Modular Cloning Toolbox for Chloroplast Biotechnology
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iotbx.cif : a comprehensive CIF toolbox
iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.
Data processing and analysis with the autoPROC toolbox
Typical topics and problems encountered during data processing of diffraction experiments are discussed and the tools provided in the autoPROC software are described. A typical diffraction experiment will generate many images and data sets from different crystals in a very short time. This creates a challenge for the high-throughput operation of modern synchrotron beamlines as well as for the subsequent data processing. Novice users in particular may feel overwhelmed by the tables, plots and numbers that the different data-processing programs and software packages present to them. Here, some of the more common problems that a user has to deal with when processing a set of images that will finally make up a processed data set are shown, concentrating on difficulties that may often show up during the first steps along the path of turning the experiment (i.e. data collection) into a model (i.e. interpreted electron density). Difficulties such as unexpected crystal forms, issues in crystal handling and suboptimal choices of data-collection strategies can often be dealt with, or at least diagnosed, by analysing specific data characteristics during processing. In the end, one wants to distinguish problems over which one has no immediate control once the experiment is finished from problems that can be remedied a posteriori. A new software package, autoPROC, is also presented that combines third-party processing programs with new tools and an automated workflow script that is intended to provide users with both guidance and insight into the offline processing of data affected by the difficulties mentioned above, with particular emphasis on the automated treatment of multi-sweep data sets collected on multi-axis goniostats.
dxtbx : the diffraction experiment toolbox
Data formats for recording X-ray diffraction data continue to evolve rapidly to accommodate new detector technologies developed in response to more intense light sources. Processing the data from single-crystal X-ray diffraction experiments therefore requires the ability to read, and correctly interpret, image data and metadata from a variety of instruments employing different experimental representations. Tools that have previously been developed to address this problem have been limited either by a lack of extensibility or by inconsistent treatment of image metadata. The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user-extensible approach to reading the data files. The library is written in a mixture of C++ and Python and is distributed as part of the cctbx under an open-source licence at http://cctbx.sourceforge.net.
Navy Enhanced Sierra Mechanics (NESM): Toolbox for predicting Navy shock and damage
Here, the US Navy is developing a new suite of computational mechanics tools (Navy Enhanced Sierra Mechanics) for the prediction of ship response, damage, and shock environments transmitted to vital systems during threat weapon encounters. NESM includes fully coupled Euler-Lagrange solvers tailored to ship shock/damage predictions. NESM is optimized to support high-performance computing architectures, providing the physics-based ship response/threat weapon damage predictions needed to support the design and assessment of highly survivable ships. NESM is being employed to support current Navy ship design and acquisition programs while being further developed for future Navy fleet needs.
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function
Computational biology is one of many scientific disciplines ripe for innovation and acceleration with the advent of high-performance computing (HPC). In recent years, the field of machine learning has also seen significant benefits from adopting HPC practices. In this work, we present a novel HPC pipeline that incorporates various machine-learning approaches for structure-based functional annotation of proteins on the scale of whole genomes. Our pipeline makes extensive use of deep learning and provides computational insights into best practices for training advanced deep-learning models for high-throughput data such as proteomics data. We showcase methodologies our pipeline currently supports and detail future tasks for our pipeline to envelop, including large-scale sequence comparison using SAdLSA and prediction of protein tertiary structures using AlphaFold2.
Resilient Adaptive Parallel sImulator for griD (RAPID): An Open Source Power System Simulation Toolbox
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A toolbox for $$q_{T}$$ and 0-jettiness subtractions at $$\hbox {N}^3\hbox {LO}$$
We derive the leading-power singular terms at three loops for both $q_T$ and 0-jettiness, $T_0$, for generic color-singlet processes. Our results provide the complete set of differential subtraction terms for $q_T$ and $T_0$ subtractions at N 3 LO, which are an important ingredient for matching N 3 LO calculations with parton showers. We obtain the full three-loop structure of the relevant beam and soft functions, which are necessary ingredients for the resummation of $q_T$ and $T_0$ at N 3 LL' and N 4 LL order, and which constitute important building blocks in other contexts as well. The nonlogarithmic boundary coefficients of the beam functions, which contribute to the integrated subtraction terms, are not yet fully known at three loops. By exploiting consistency relations between different factorization limits, we derive results for the $q_T$ and $T_0$ beam function coefficients at N 3 LO in the z→1 threshold limit, and we also estimate the size of the unknown terms beyond threshold.