936 research outputs found
A Streaming Multi-GPU Implementation of Image Simulation Algorithms for Scanning Transmission Electron Microscopy
Simulation of atomic resolution image formation in scanning transmission
electron microscopy can require significant computation times using traditional
methods. A recently developed method, termed plane-wave reciprocal-space
interpolated scattering matrix (PRISM), demonstrates potential for significant
acceleration of such simulations with negligible loss of accuracy. Here we
present a software package called Prismatic for parallelized simulation of
image formation in scanning transmission electron microscopy (STEM) using both
the PRISM and multislice methods. By distributing the workload between multiple
CUDA-enabled GPUs and multicore processors, accelerations as high as 1000x for
PRISM and 30x for multislice are achieved relative to traditional multislice
implementations using a single 4-GPU machine. We demonstrate a potentially
important application of Prismatic, using it to compute images for atomic
electron tomography at sufficient speeds to include in the reconstruction
pipeline. Prismatic is freely available both as an open-source CUDA/C++ package
with a graphical user interface and as a Python package, PyPrismatic
Laser-Accelerated proton beams as diagnostics for cultural heritage
This paper introduces the first use of laser-generated proton beams as diagnostic for materials of interest in the domain of Cultural Heritage. Using laser-accelerated protons, as generated by interaction of a high-power short-pulse laser with a solid target, we can produce proton-induced X-ray emission spectroscopies (PIXE). By correctly tuning the proton flux on the sample, we are able to perform the PIXE in a single shot without provoking more damage to the sample than conventional methodologies. We verify this by experimentally irradiating materials of interest in the Cultural Heritage with laser-accelerated protons and measuring the PIXE emission. The morphological and chemical analysis of the sample before and after irradiation are compared in order to assess the damage provoked to the artifact. Montecarlo simulations confirm that the temperature in the sample stays safely below the melting point. Compared to conventional diagnostic methodologies, laser-driven PIXE has the advantage of being potentially quicker and more efficien
Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy
Atom probe tomography, and related methods, probe the composition and the three-dimensional architecture of materials. The software tools which microscopists use, and how these tools are connected into workflows, make a substantial contribution to the accuracy and precision of such material characterization experiments. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced it is useful to join forces. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe microscopy software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results
IMP Science Gateway: from the Portal to the Hub of Virtual Experimental Labs in Materials Science
"Science gateway" (SG) ideology means a user-friendly intuitive interface
between scientists (or scientific communities) and different software
components + various distributed computing infrastructures (DCIs) (like grids,
clouds, clusters), where researchers can focus on their scientific goals and
less on peculiarities of software/DCI. "IMP Science Gateway Portal"
(http://scigate.imp.kiev.ua) for complex workflow management and integration of
distributed computing resources (like clusters, service grids, desktop grids,
clouds) is presented. It is created on the basis of WS-PGRADE and gUSE
technologies, where WS-PGRADE is designed for science workflow operation and
gUSE - for smooth integration of available resources for parallel and
distributed computing in various heterogeneous distributed computing
infrastructures (DCI). The typical scientific workflows with possible scenarios
of its preparation and usage are presented. Several typical use cases for these
science applications (scientific workflows) are considered for molecular
dynamics (MD) simulations of complex behavior of various nanostructures
(nanoindentation of graphene layers, defect system relaxation in metal
nanocrystals, thermal stability of boron nitride nanotubes, etc.). The user
experience is analyzed in the context of its practical applications for MD
simulations in materials science, physics and nanotechnologies with available
heterogeneous DCIs. In conclusion, the "science gateway" approach - workflow
manager (like WS-PGRADE) + DCI resources manager (like gUSE)- gives opportunity
to use the SG portal (like "IMP Science Gateway Portal") in a very promising
way, namely, as a hub of various virtual experimental labs (different software
components + various requirements to resources) in the context of its practical
MD applications in materials science, physics, chemistry, biology, and
nanotechnologies.Comment: 6 pages, 5 figures, 3 tables; 6th International Workshop on Science
Gateways, IWSG-2014 (Dublin, Ireland, 3-5 June, 2014). arXiv admin note:
substantial text overlap with arXiv:1404.545
Review of the Synergies Between Computational Modeling and Experimental Characterization of Materials Across Length Scales
With the increasing interplay between experimental and computational
approaches at multiple length scales, new research directions are emerging in
materials science and computational mechanics. Such cooperative interactions
find many applications in the development, characterization and design of
complex material systems. This manuscript provides a broad and comprehensive
overview of recent trends where predictive modeling capabilities are developed
in conjunction with experiments and advanced characterization to gain a greater
insight into structure-properties relationships and study various physical
phenomena and mechanisms. The focus of this review is on the intersections of
multiscale materials experiments and modeling relevant to the materials
mechanics community. After a general discussion on the perspective from various
communities, the article focuses on the latest experimental and theoretical
opportunities. Emphasis is given to the role of experiments in multiscale
models, including insights into how computations can be used as discovery tools
for materials engineering, rather than to "simply" support experimental work.
This is illustrated by examples from several application areas on structural
materials. This manuscript ends with a discussion on some problems and open
scientific questions that are being explored in order to advance this
relatively new field of research.Comment: 25 pages, 11 figures, review article accepted for publication in J.
Mater. Sc
Deep Learning for Automated Experimentation in Scanning Transmission Electron Microscopy
Machine learning (ML) has become critical for post-acquisition data analysis
in (scanning) transmission electron microscopy, (S)TEM, imaging and
spectroscopy. An emerging trend is the transition to real-time analysis and
closed-loop microscope operation. The effective use of ML in electron
microscopy now requires the development of strategies for microscopy-centered
experiment workflow design and optimization. Here, we discuss the associated
challenges with the transition to active ML, including sequential data analysis
and out-of-distribution drift effects, the requirements for the edge operation,
local and cloud data storage, and theory in the loop operations. Specifically,
we discuss the relative contributions of human scientists and ML agents in the
ideation, orchestration, and execution of experimental workflows and the need
to develop universal hyper languages that can apply across multiple platforms.
These considerations will collectively inform the operationalization of ML in
next-generation experimentation.Comment: Review Articl
Laser-Accelerated proton beams as diagnostics for cultural heritage
This paper introduces the first use of laser-generated proton beams as diagnostic for materials of interest in the domain of Cultural Heritage. Using laser-accelerated protons, as generated by interaction of a high-power short-pulse laser with a solid target, we can produce proton-induced X-ray emission spectroscopies (PIXE). By correctly tuning the proton flux on the sample, we are able to perform the PIXE in a single shot without provoking more damage to the sample than conventional methodologies. We verify this by experimentally irradiating materials of interest in the Cultural Heritage with laser-accelerated protons and measuring the PIXE emission. The morphological and chemical analysis of the sample before and after irradiation are compared in order to assess the damage provoked to the artifact. Montecarlo simulations confirm that the temperature in the sample stays safely below the melting point. Compared to conventional diagnostic methodologies, laser-driven PIXE has the advantage of being potentially quicker and more efficien
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