A5052163488- Advanced X-ray Imaging Techniques
- Advanced Electron Microscopy Techniques and Applications
- X-ray Spectroscopy and Fluorescence Analysis
- Enzyme Structure and Function
- Particle Accelerators and Free-Electron Lasers
- Scientific Computing and Data Management
- Material Dynamics and Properties
- Phase Equilibria and Thermodynamics
- Distributed and Parallel Computing Systems
- Advanced Thermodynamics and Statistical Mechanics
- Advanced Mathematical Theories and Applications
- Particle Detector Development and Performance
- Korean Peninsula Historical and Political Studies
- scientometrics and bibliometrics research
- Magnetic and Electromagnetic Effects
- Mathematics, Computing, and Information Processing
- Digital Transformation in Law
- Advanced Data Storage Technologies
- Laser Design and Applications
- nanoparticles nucleation surface interactions
- Genetics, Bioinformatics, and Biomedical Research
- Spectroscopy and Quantum Chemical Studies
- Microbial Community Ecology and Physiology
- Research Data Management Practices
- Advanced Measurement and Metrology Techniques
Kurchatov Institute
2015-2024
Nova Institut
2015
Abstract The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement significantly more experimental data per day than was previously possible. European XFEL is expected to provide 27,000 pulses second, over two orders magnitude any other XFEL. increased pulse rate a key enabling factor for single-particle diffractive imaging, which relies on averaging weak diffraction signal from single biological...
The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline LCLS as part SPI initiative is presented here. A workflow for three-dimensional virus reconstruction PR772 bacteriophage from measured data developed. It consists several well defined steps including single-hit diffraction classification, refined filtering classified data, scattered intensity experimental patterns by orientation determination and final electron density without symmetry constraints....
Abstract Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without need crystallization. In an effort to further develop technique, we present a dataset of coherent soft images Coliphage PR772 virus, collected at Atomic Molecular Optics (AMO) beamline with pnCCD detectors in LAMP instrument Linac Coherent Light Source. The diameter ranges 65–70 nm, which is considerably smaller than previously reported ~600 nm Mimivirus....
Modern X-ray free-electron lasers (XFELs) operating at high repetition rates produce a tremendous amount of data. It is great challenge to classify this information and reduce the initial data set manageable size for further analysis. Here an approach classification diffraction patterns measured in prototypical diffract-and-destroy single-particle imaging experiments XFELs presented. proposed that are classified on basis parameters take into account underlying physics specific relations...
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at Atomic, Molecular and Optical Science instrument Linac Coherent Light Source as part SPI initiative. Existing methods were modified to cope with shortcomings experimental data: inaccessibility information from half detector small fraction single hits. The general workflow was upgraded expectation-maximization...
Single particle imaging (SPI) is a promising method for native structure determination which has undergone fast progress with the development of X-ray Free-Electron Lasers. Large amounts data are collected during SPI experiments, driving need automated analysis. The necessary analysis pipeline number steps including binary object classification (single versus multiple hits). Classification and detection areas where deep neural networks currently outperform other approaches. In this work, we...
In this paper we present the design and deployment details for Single Particle Imaging (SPI) experiments data analysis pipeline in Kubernetes infrastructure. We have analyzed various software usage patterns different payloads. Components of include traditional HPC (MPI-based) applications, applications which require GPU computations, GUI-based can be parallelized naturally by dividing into several independent parts (Data parallelism). For every payload type individual approach was proposed.
The ability to investigate 3D structure of biomolecules, such as proteins and viruses, is essential in biology medicine. With the invention super-bright X-ray free electron lasers (e.g. European XFEL Linac Coherent Light Source (LCLS)) Single Particle Imaging (SPI) approach allows reconstruct structures from many 2D diffraction images produced experiment by X-rays scattered on biomolecule exposed different orientations. In same time, there are still challenging problems setup, sample...
The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement significantly more experimental data per day than was previously possible. European XFEL will soon provide 27,000 pulses second, two orders magnitude any other XFEL. increased pulse rate is a key enabling factor for single-particle diffractive imaging, which relies on averaging weak diffraction signal from single biological particles. Taking full...
Abstract In accordance with the order of President Russian Federation, National Research Center “Kurchatov Institute” is creating Genomic Information Database (NGID). According to amendments Federal Law dated December 29, 2022, it mandatory for organizations involved in genetic engineering and production or supply genetically engineered organisms products obtained their use deposit information NGID. It planned that NGID will become a key element infrastructure research development Russia,...
Invention of Coherent X-ray Diffractive Imaging (CXDI) technique allows to reconstruct inner structure nanoparticles, such as proteins and viruses, with 1 Å resolution. In CXDI experiments, free electron laser radiation scatters at sample object under study a diffraction image is recorded. On basis many recorded images, original 3D reconstructed. However, not all images can be used for reconstruction, are empty, others contain pattern some contaminant or include contributions several...
The new free-electron lasers (FELs) open up possibilities for the study of biological particles such as proteins and viruses. Development data analysis algorithms requires large datasets diffraction images produced by simulation. Existing programs are not capable effective use modern computational resources, especially adapted to hybrid architecture with GPU. We explored possibility performance increase in SPSIM program simulation images, using CUDA technology. Also, we have implemented...
About 1% of diffraction images produced in coherent X-ray imaging experiments originate from a single particle interest and only those are suitable for structure reconstruction. Other contain contributions multiple particles, water or some contaminant. Selection is required. A new classification method that based on cross-correlation analysis were developed. The was successfully applied to the experimental data, PBCV-1 virus T4 bacteriophage. In this article we present results seven...
В работе представлены результаты применения алгоритмов машинного обучения: метода главных компонент и опорных векторов для классификации дифракционных изображений, полученных в экспериментах на лазерах свободных электронах. Показана высокая эффективность такого подхода с использованием модельных данных дифракции лазерного пучка капсиде аденовируса вируса катаральной лихорадки, которых учтены условия реального эксперимента электронах, такие как шум особенности используемых детекторов.
Jupyter notebook is a popular framework for interactive application development and data analysis. Deployment of JupyterHub on supercomputer infrastructure would allow to combine high computing power large storage capacity with convenience ease use end users. In this work we present the architecture deployment details in Kurchatov Institute infrastructure. our setup combined CEPHfs system, FreeIPA user management customized CUDA-compatible image worker applications used Kubernetes as...