One of the essential points of the direct-method single-wavelength anomalous diffraction （SAD） phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respec...One of the essential points of the direct-method single-wavelength anomalous diffraction （SAD） phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respectively at φh″＋｜△φh｜ and φh″-｜△φh｜. The probability for △φh being positive （P＋） can be derived based on the Cochran distribution in direct methods. Hence the SAD phase ambiguity can be resolved by multiplying the Gaussian function peaked at φh″＋｜△φh｜ with P＋ and multiplying the Gaussian function peaked at φh″-｜△φh｜ with P_ （=1- P＋）. The direct-method SAD h phasing has been proved powerful in breaking SAD phase ambiguities, in particular when anomalous-scattering signals are weak. However, the approximation of bimodal phase distributions by the sum of two Gaussian functions introduces considerable errors. In this paper we show that a much better approximation can be achieved by replacing the two Gaussian functions with two von Mises distributions. Test results showed that this leads to significant improvement on the efficiency of direct-method SAD-phasing.展开更多
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
Optical phase-gradient metasurfaces have garnered significant attention for enabling flexible light manipulation,with applications across diverse domains.In this work,we will demonstrate that the metasurfaces with pha...Optical phase-gradient metasurfaces have garnered significant attention for enabling flexible light manipulation,with applications across diverse domains.In this work,we will demonstrate that the metasurfaces with phase gradient modulation can be used to achieve illusion optics,featuring the advantages of simple geometric structure and feasible implementation compared with the well-known transformation optics method.The underlying mechanism is the anomalous diffraction law caused by the phase gradient,which provides a theoretical basis for freely manipulating the propagation path of light.By considering a specific example,we will demonstrate that the phase gradient can transform spatial coordinates in real space into illusion space,thereby converting a plane in real space into a curved surface structure in illusion space to achieve the illusion effect.This approach provides a viable alternative to transformation optics for designing illusion devices.展开更多
Considering the pivotal role of single-wavelength anomalous diffraction(SAD) in macromolecular crystallography,our objective was to introduce DSAS,a novel program designed for efficient anomalous scattering substructu...Considering the pivotal role of single-wavelength anomalous diffraction(SAD) in macromolecular crystallography,our objective was to introduce DSAS,a novel program designed for efficient anomalous scattering substructure determination.DSAS stands out with its core components:a modified phase-retrieval algorithm and automated parameter tuning.The software boasts an intuitive graphical user interface(GUI),facilitating seamless input of essential data and real-time monitoring.Extensive testing on DSAS has involved diverse datasets,encompassing proteins,nucleic acids,and various anomalous scatters such as sulfur(S),selenium(Se),metals,and halogens.The results confirm DSAS’s exceptional performance in accurately determining heavy atom positions,making it a highly effective tool in the field.展开更多
基金Project supported by the Innovation Foundation of the Chinese Academy of Sciences and by the National Basic Research Program of China(Grant No.2002CB713801)
文摘One of the essential points of the direct-method single-wavelength anomalous diffraction （SAD） phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respectively at φh″＋｜△φh｜ and φh″-｜△φh｜. The probability for △φh being positive （P＋） can be derived based on the Cochran distribution in direct methods. Hence the SAD phase ambiguity can be resolved by multiplying the Gaussian function peaked at φh″＋｜△φh｜ with P＋ and multiplying the Gaussian function peaked at φh″-｜△φh｜ with P_ （=1- P＋）. The direct-method SAD h phasing has been proved powerful in breaking SAD phase ambiguities, in particular when anomalous-scattering signals are weak. However, the approximation of bimodal phase distributions by the sum of two Gaussian functions introduces considerable errors. In this paper we show that a much better approximation can be achieved by replacing the two Gaussian functions with two von Mises distributions. Test results showed that this leads to significant improvement on the efficiency of direct-method SAD-phasing.
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supported by the National Natural Science Foundation of China (Grant Nos.12274313 and 62375234)the Gusu Leading Talent Plan for Scientific and Technological Innovation and Entrepreneurship (Grant No.ZXL2024400)。
文摘Optical phase-gradient metasurfaces have garnered significant attention for enabling flexible light manipulation,with applications across diverse domains.In this work,we will demonstrate that the metasurfaces with phase gradient modulation can be used to achieve illusion optics,featuring the advantages of simple geometric structure and feasible implementation compared with the well-known transformation optics method.The underlying mechanism is the anomalous diffraction law caused by the phase gradient,which provides a theoretical basis for freely manipulating the propagation path of light.By considering a specific example,we will demonstrate that the phase gradient can transform spatial coordinates in real space into illusion space,thereby converting a plane in real space into a curved surface structure in illusion space to achieve the illusion effect.This approach provides a viable alternative to transformation optics for designing illusion devices.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.32371280 and T2350011)。
文摘Considering the pivotal role of single-wavelength anomalous diffraction(SAD) in macromolecular crystallography,our objective was to introduce DSAS,a novel program designed for efficient anomalous scattering substructure determination.DSAS stands out with its core components:a modified phase-retrieval algorithm and automated parameter tuning.The software boasts an intuitive graphical user interface(GUI),facilitating seamless input of essential data and real-time monitoring.Extensive testing on DSAS has involved diverse datasets,encompassing proteins,nucleic acids,and various anomalous scatters such as sulfur(S),selenium(Se),metals,and halogens.The results confirm DSAS’s exceptional performance in accurately determining heavy atom positions,making it a highly effective tool in the field.
