In this paper, we present a highly efficient structure determination pipeline software suite(X^2 DF) that is based on the "Parameter space screening" method, by combining the popular crystallographic structu...In this paper, we present a highly efficient structure determination pipeline software suite(X^2 DF) that is based on the "Parameter space screening" method, by combining the popular crystallographic structure determination programs and high-performance parallel computing. The phasing method employed in X^2 DF is based on the single-wavelength anomalous diffraction(SAD) theory. In the X^2 DF, the choice of crystallographic software, the input parameters to this software and the results display layout, are all parameters which users can select and screen automatically. Users may submit multiple structure determination jobs each time, and each job uses a slightly different set of input parameters or programs. Upon completion, the results of the calculation performed can be displayed, harvested, and analyzed by using the graphical user interface(GUI) of the system. We have applied the X^2 DF successfully to many cases including the cases that the structure solutions fail to be yielded by using manual approaches.展开更多
To achieve de novo protein structure determination of challenging cases, multi-wavelength anomalous diffraction(MAD) and multiple isomorphous replacement(MIR) phasing can be powerful tools to obtain low-resolution ini...To achieve de novo protein structure determination of challenging cases, multi-wavelength anomalous diffraction(MAD) and multiple isomorphous replacement(MIR) phasing can be powerful tools to obtain low-resolution initial phases from heavy-atom derivative datasets, then phase extension is needed against high-resolution data to obtain accurate structures.In this context, we propose a direct-methods procedure here that could improve the initial low-resolution MAD/MIR phase quality.And accordingly, an automated process for extending initial phases to high resolution is also described.These two procedures are both implanted in the newly released IPCAS pipeline.Three cases are used to perform the test, including one set of 4.17 ? MAD data from a membrane protein and two sets of MAD/MIR data with derivatives truncated down to 6.80 ? and 6.90 ?, respectively.All the results have shown that the initial phases generated from the direct-methods procedure are better than that from the conventional MAD/MIR methods.The automated phase extensions for the latter two cases starting from 6.80 ? to 3.00 ? and 6.90 ? to 2.80 ? are proved to be successful, leading to complete models.This may provide convenient and reliable tools for phase improvement and phase extension in difficult low-resolution tasks.展开更多
Calcium silicate slag is the residue of process of pre-desilication alkali lime sintering applied in the high-alumina fly ash to extract the alumina.The quantitative phase analysis(QPA) of the calcium silicate slag ha...Calcium silicate slag is the residue of process of pre-desilication alkali lime sintering applied in the high-alumina fly ash to extract the alumina.The quantitative phase analysis(QPA) of the calcium silicate slag has been performed by the Rietveld method based on the powder X-ray diffraction(XRD) with the aid of noncommercial software GSAS-EXPGUI.A known weight of crystalline internal standard(10% CaF_2) was added to the calcium silicate slag to calculate the fraction of amorphous phase and other crystalline phases on an absolute basis.Besides,the calcium silicate slag was characterized by X-ray fluorescence(XRF) and thermo gravimetric(TG) differential scanning calorimetry(DSC) to test the QPA results and investigate its other characters.Finally,the results show that the amorphous fraction is 17.5%(hereinafter,the percentages refer to the mass fraction),and the major crystalline phases detected in the calcium silicate slag consist of 23.5% Beta-Ca_2 SiO_4,10.0% bredigite,10.3% Ca_3Al_2O_6(C_3A) and 21.6% CaCO_3.展开更多
Inversion of droplet size distribution in two-phase flow from light scattering has been considered involved because it is in general reduced to the solution of Fredholm integral equation of the first kind that was alw...Inversion of droplet size distribution in two-phase flow from light scattering has been considered involved because it is in general reduced to the solution of Fredholm integral equation of the first kind that was always ill-posed. By using the Rosin-Rammler distributiona priori as the particulate size distribution model in the liquid-gas two-phase flow, a method via the solution of a two-parameter nonlinear programming problem to determine the droplet size distribution has been developed. A measurement system based on the technique is designed and applied in the shock test of blades of steam turbine. 100-hours continuous monitoring of the droplets in the liquid-gas two-phase flow of 8.0 Pa and 120 °C was performed and the details of the experiments are given out. It is shown that the technique is simple and efficient for in-situ real time measuring droplets in the liquid-gas two-phase flow.展开更多
Coherent Diffraction Imaging(CDI)is an experimental technique to image isolated structures by recording the scattered light.The sample density can be recovered from the scattered field through a Fourier Transform oper...Coherent Diffraction Imaging(CDI)is an experimental technique to image isolated structures by recording the scattered light.The sample density can be recovered from the scattered field through a Fourier Transform operation.However,the phase of the field is lost during the measurement and has to be algorithmically retrieved.Here we present SPRING,an analysis framework tailored to X-ray Free Electron Laser(XFEL)single-shot single-particle diffraction data that implements the Memetic Phase Retrieval method to mitigate the shortcomings of conventional algorithms.We benchmark the approach on data acquired in two experimental campaigns at SwissFEL and European XFEL.Results reveal unprecedented stability and resilience of the algorithm’s behavior on the input parameters,and the capability of identifying the solution in conditions hardly treatable with conventional methods.A user-friendly implementation of SPRING is released as open-source software,aiming at being a reference tool for the CDI community at XFEL and synchrotron facilities.展开更多
文摘In this paper, we present a highly efficient structure determination pipeline software suite(X^2 DF) that is based on the "Parameter space screening" method, by combining the popular crystallographic structure determination programs and high-performance parallel computing. The phasing method employed in X^2 DF is based on the single-wavelength anomalous diffraction(SAD) theory. In the X^2 DF, the choice of crystallographic software, the input parameters to this software and the results display layout, are all parameters which users can select and screen automatically. Users may submit multiple structure determination jobs each time, and each job uses a slightly different set of input parameters or programs. Upon completion, the results of the calculation performed can be displayed, harvested, and analyzed by using the graphical user interface(GUI) of the system. We have applied the X^2 DF successfully to many cases including the cases that the structure solutions fail to be yielded by using manual approaches.
基金Project supported by the National Basic Research Program of China(Grant No.2011CB911100)of the Ministry of Science and Technology of China
文摘To achieve de novo protein structure determination of challenging cases, multi-wavelength anomalous diffraction(MAD) and multiple isomorphous replacement(MIR) phasing can be powerful tools to obtain low-resolution initial phases from heavy-atom derivative datasets, then phase extension is needed against high-resolution data to obtain accurate structures.In this context, we propose a direct-methods procedure here that could improve the initial low-resolution MAD/MIR phase quality.And accordingly, an automated process for extending initial phases to high resolution is also described.These two procedures are both implanted in the newly released IPCAS pipeline.Three cases are used to perform the test, including one set of 4.17 ? MAD data from a membrane protein and two sets of MAD/MIR data with derivatives truncated down to 6.80 ? and 6.90 ?, respectively.All the results have shown that the initial phases generated from the direct-methods procedure are better than that from the conventional MAD/MIR methods.The automated phase extensions for the latter two cases starting from 6.80 ? to 3.00 ? and 6.90 ? to 2.80 ? are proved to be successful, leading to complete models.This may provide convenient and reliable tools for phase improvement and phase extension in difficult low-resolution tasks.
基金the National Natural Science Foundation of China(Nos.51302012 and 51274042)the China Postdoctoral Science Foundation Funded Project(No.2016T90034)the Inner Mongolia Science and Technology Major Projects 2013
文摘Calcium silicate slag is the residue of process of pre-desilication alkali lime sintering applied in the high-alumina fly ash to extract the alumina.The quantitative phase analysis(QPA) of the calcium silicate slag has been performed by the Rietveld method based on the powder X-ray diffraction(XRD) with the aid of noncommercial software GSAS-EXPGUI.A known weight of crystalline internal standard(10% CaF_2) was added to the calcium silicate slag to calculate the fraction of amorphous phase and other crystalline phases on an absolute basis.Besides,the calcium silicate slag was characterized by X-ray fluorescence(XRF) and thermo gravimetric(TG) differential scanning calorimetry(DSC) to test the QPA results and investigate its other characters.Finally,the results show that the amorphous fraction is 17.5%(hereinafter,the percentages refer to the mass fraction),and the major crystalline phases detected in the calcium silicate slag consist of 23.5% Beta-Ca_2 SiO_4,10.0% bredigite,10.3% Ca_3Al_2O_6(C_3A) and 21.6% CaCO_3.
文摘Inversion of droplet size distribution in two-phase flow from light scattering has been considered involved because it is in general reduced to the solution of Fredholm integral equation of the first kind that was always ill-posed. By using the Rosin-Rammler distributiona priori as the particulate size distribution model in the liquid-gas two-phase flow, a method via the solution of a two-parameter nonlinear programming problem to determine the droplet size distribution has been developed. A measurement system based on the technique is designed and applied in the shock test of blades of steam turbine. 100-hours continuous monitoring of the droplets in the liquid-gas two-phase flow of 8.0 Pa and 120 °C was performed and the details of the experiments are given out. It is shown that the technique is simple and efficient for in-situ real time measuring droplets in the liquid-gas two-phase flow.
基金the Swiss National Science Foundation (via grant no. 200021E_193642, grant no. 200021-232306, and the NCCR MUST)ETH Zurich (via collaborative grant 23-2ETH-050) for financial support+7 种基金MP, OV, and MB further acknowledge the Research Council of Finland for financial support (including projects 326291, 330118, and 341288)TF acknowledges funding by the Deutsche Forschungsgemeinschaft within CRC 1477 “Light-Matter Interactions at Interfaces” (project number 441234705)PHWS acknowledges support from the Swedish Research Council through project 2018-00740FRNCM acknowledges the Swedish Research Council (2018-00234 and 2019-06092) and the Carl Tryggers Stiftelse för Vetenskaplig Forskning (CTS 19-227)JAS acknowledges the Swedish Research Council (2023-06350)the Göran Gustafsson Foundation (2044)the Carl Tryggers Stiftelse för Vetenskaplig Forskning (CTS 21-1427)The Maloja instrument received funding from the Swiss National Science Foundation through R’Equip Grant No. 206021_182988. We thank the IT Services Group (ISG) of the Department of Physics at ETH Zurich for the excellent support and management of the computing hardware on which the spring software has been developed and tested.
文摘Coherent Diffraction Imaging(CDI)is an experimental technique to image isolated structures by recording the scattered light.The sample density can be recovered from the scattered field through a Fourier Transform operation.However,the phase of the field is lost during the measurement and has to be algorithmically retrieved.Here we present SPRING,an analysis framework tailored to X-ray Free Electron Laser(XFEL)single-shot single-particle diffraction data that implements the Memetic Phase Retrieval method to mitigate the shortcomings of conventional algorithms.We benchmark the approach on data acquired in two experimental campaigns at SwissFEL and European XFEL.Results reveal unprecedented stability and resilience of the algorithm’s behavior on the input parameters,and the capability of identifying the solution in conditions hardly treatable with conventional methods.A user-friendly implementation of SPRING is released as open-source software,aiming at being a reference tool for the CDI community at XFEL and synchrotron facilities.
