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Long, Fei

Publications and source records attributed to Long, Fei.

22 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Deformation mechanism study of a hot rolled Zr-2.5Nb alloy by transmission electron microscopy. I. Dislocation microstructures in as-received state and at different plastic strains

Thin foil dog bone samples prepared from a hot rolled Zr-2.5Nb alloy have been deformed by tensile deformation to different plastic strains. The development of slip traces during loading was observed in situ through SEM, revealing that deformation starts preferentially in certain sets of grains during the elastic-plastic transition region. TEM characterization showed that sub-grain boundaries formed during hot rolling consisted of screw 〈a〉 dislocations or screw 〈c〉 and 〈a〉 dislocations. Prismatic 〈a〉 dislocations with large screw or edge components have been identified from the sample with 0.5% plastic strain. Basal 〈a〉 and pyramidal 〈c + a〉 dislocations were found in the sample that had been deformed with 1.5% plastic strain, implying that these dislocations require larger stresses to be activated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions. The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

Low-resolution refinement tools in REFMAC5

Low-resolution refinement tools implemented in REFMAC5 are described, including the use of external structural restraints, helical restraints and regularized anisotropic map sharpening. Two aspects of low-resolution macromolecular crystal structure analysis are considered: (i) the use of reference structures and structural units for provision of structural prior information and (ii) map sharpening in the presence of noise and the effects of Fourier series termination. The generation of interatomic distance restraints by ProSMART and their subsequent application in REFMAC5 is described. It is shown that the use of such external structural information can enhance the reliability of derived atomic models and stabilize refinement. The problem of map sharpening is considered as an inverse deblurring problem and is solved using Tikhonov regularizers. It is demonstrated that this type of map sharpening can automatically produce a map with more structural features whilst maintaining connectivity. Tests show that both of these directions are promising, although more work needs to be performed in order to further exploit structural information and to address the problem of reliable electron-density calculation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗