Shanghai University

About: Shanghai University is a education organization based out in Shanghai, Shanghai, China. It is known for research contribution in the topics: Microstructure & Graphene. The organization has 59583 authors who have published 56840 publications receiving 753549 citations. The organization is also known as: Shànghǎi Dàxué.

A coupling method of a homotopy technique and a perturbation technique for non-linear problems

Abstract: In this paper, a coupling method of a homotopy technique and a perturbation technique is proposed to solve non-linear problems. In contrast to the traditional perturbation methods, the proposed method does not require a small parameter in the equation. In this method, according to the homotopy technique, a homotopy with an imbedding parameter p∈[0, 1] is constructed, and the imbedding parameter is considered as a “small parameter”. So the proposed method can take full advantage of the traditional perturbation methods. Some examples are given. The results reveal that the new method is very effective and simple.

Real-space refinement in PHENIX for cryo-EM and crystallography.

Abstract: This article describes the implementation of real-space refinement in the phenixreal_space_refine program from the PHENIX suite The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available In addition to standard restraints on covalent geometry, phenixreal_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 A or better shows significant improvement of the models and of the fit of these models to the target maps

On the origin and continuing evolution of SARS-CoV-2

Abstract: The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses had two major lineages (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. We found that L lineage was more prevalent than the S lineage within the limited patient samples we examined. The implication of these evolutionary changes on disease etiology remains unclear. These findings strongly underscores the urgent need for further comprehensive studies that combine viral genomic data, with epidemiological studies of coronavirus disease 2019 (COVID-19).