检索结果-南通市图书馆

Single-cell omics: experimental workflow, data analyses and applications

Science China Life sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University key laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang key laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine key laboratory of Advanced Theory and Application in Statistics and Data Science-moe School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

来源：

同方期刊数据库评论

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

INEXACT TWO-GRID METHODS FOR EIGENVALUE PROBLEMS

引用

Journal of computational Mathematics 2015年第6期33卷 557-575页

作者： Qun Gu Weiguo Gao moe key laboratory of computational physical sciences and School of Mathematical sciences Fudan Univecsity Shanghai 200433 China

We discuss the inexact two-grid methods for solving eigenvalue problems, including both partial differential and integral equations. Instead of solving the linear system exactly in both traditional two-grid and accelerated two-grid method, we point out that it is enough to apply an inexact solver to the fine grid problems, which will cut down the computational cost. Different stopping criteria for both methods are developed for keeping the optimality of the resulting solution. Numerical examples are provided to verify our theoretical analyses.

关键词： Inexact Two-grid Eigenvalue Eigenvector Finite element method Conver-gence rate.

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Dynamical Coupling Atomistic and Continuum Simulations

引用

Communications in computational Physics 2011年第10期10卷 1305-1314页

作者： Guowu Ren Dier Zhang Xin-Gao Gong key laboratory for computational physical sciences(moe) Fudan UniversityShanghai 200433China

We propose a newmultiscalemethod that couplesmolecular dynamics simulations(MD)at the atomic scale and finite element simulations(FE)at the continuum *** constructing the mass matrix and stiffness matrix dependent on coarsening of grids,we find a general form of the equations of motion for the atomic and continuum *** order to improve the simulation at finite temperatures,we propose a low-pass phonon filter near the interface between the atomic and continuum regions,which is transparent for low frequency phonons,but dampens the high frequency phonons.

关键词： Multiscale method finite element phonon filter method

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Directly Determining the Interface Structure and Band Offset of a Large-Lattice-Mismatched CdS/CdTe Heterostructure

引用

Chinese Physics Letters 2020年第9期37卷 46-51页

作者： Quanyin Tang Ji-Hui Yang Zhi-Pan Liu Xin-Gao Gong key laboratory for computational physical sciences(moe) State Key Laboratory of Surface PhysicsDepartment of PhysicsFudan UniversityShanghai 200433China key laboratory for computational physical sciences(moe) Shanghai Key Laboratory of Molecular Catalysis and Innovative MaterialsDepartment of ChemistryFudan UniversityShanghai 200433China Shanghai Qi Zhi Institute Shanghai 200232China

The CdS/CdTe heterojunction plays an important role in determining the energy conversion efficiency of CdTe solar ***,the interface structure remains unknown,due to the large lattice mismatch between CdS and CdTe,posing great challenges to achieving an understanding of its interfacial *** combining a neuralnetwork-based machine-learning method and the stochastic surface walking-based global optimization method,we first train a neural network potential for CdSTe systems with demonstrated robustness and *** on the above potential,we then use simulated annealing to obtain the optimal structure of the CdS/CdTe *** find that the most stable structure has the features of both bulks and *** the obtained structure,we directly calculate the band offset between CdS and CdTe by aligning the core levels in the heterostructure with those in the bulks,using one-shot first-principles *** calculated band offset is 0.55 eV,in comparison with 0.70 eV,obtained using other indirect *** obtained interface structure should prove useful for further study of the properties of CdTe/CdS *** work also presents an example which is applicable to other complex interfaces.

关键词： interface structure Lattice

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

Quantum anomalous Hall effect in real materials

引用

Chinese Physics B 2016年第11期25卷 41-53页

作者：张加永赵宝周通杨中芹 State key laboratory of Surface Physics and key laboratory for computational physical sciences (moe) & Department of Physics Fudan University Collaborative Innovation Center of Advanced Microstructures Fudan University

Under a strong magnetic field,the quantum Hall（QH） effect can be observed in two-dimensional electronic gas *** the quantized Hall conductivity is acquired in a system without the need of an external magnetic field,then it will give rise to a new quantum state,the quantum anomalous Hall（QAH） *** QAH state is a novel quantum state that is insulating in the bulk but exhibits unique conducting edge states topologically protected from backscattering and holds great potential for applications in low-power-consumption *** realization of the QAH effect in real materials is of great *** this paper,we systematically review the theoretical proposals that have been brought forward to realize the QAH effect in various real material systems or structures,including magnetically doped topological insulators,graphene-based systems,silicene-based systems,two-dimensional organometallic frameworks,quantum wells,and functionalized Sb（111） monolayers,*** paper can help our readers to quickly grasp the recent developments in this field.

关键词： systematically anomalous topological insulating hollow quickly doping realization permission bands

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

An accurate single descriptor for ion–π interactions

引用

National Science Review 2020年第6期7卷 1036-1045页

作者： Zhangyun Liu Zheng Chen Jinyang Xi Xin Xu Collaborative Innovation Center of Chemistry for Energy Materials Key Laboratory of Molecular Catalysis and Innovative Materials MOE Key Laboratory of Computational Physical Sciences Department of Chemistry Fudan University

Non-covalent interactions between ions and π systems play an important role in molecular recognition,catalysis and biology. To guide the screen and design for artificial hosts, catalysts and drug delivery,understanding the physical nature of ion–π complexes via descriptors is indispensable. However, even with multiple descriptors that contain the leading term of electrostatic and polarized interactions, the quantitative description for the binding energies(BEs) of ion–π complexes is still lacking because of the intrinsic shortcomings of the commonly used descriptors. Here, we have shown that the impartment of orbital details into the electrostatic energy(coined as OEE) makes an excellent single descriptor for BEs of not only spherical, but also multiply-shaped, ion–π systems, highlighting the importance of an accurate description of the electrostatic interactions. Our results have further demonstrated that OEEs from a low-level method could be calibrated to BEs from a high-level method, offering a powerful practical strategy for an accurate prediction of a set of ion–π interactions.

关键词： ion–π interactions physical nature descriptors electrostatics multiply-shaped ions

来源：

同方期刊数据库评论

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Density-functional theory study of the effect of pressure on the elastic properties of CaB_6

引用

Chinese Physics B 2013年第7期22卷 420-425页

作者：韩晗 Surface Physics laboratory (National key laboratory) Key Laboratory of Computational Physical Sciencesand Department of PhysicsFudan University

Under high pressure, the long believed single-phase material CaB6 was latterly discovered to have a new phase tI56. Based on the density-functional theory, the pressure effects on the structural and elastic properties of CaB6 are obtained. The calculated bulk, shear, and Young’s moduli of the recently synthesized high pressure phase tI56-CaB6 are larger than those of the low pressure phase. Moreover, the high pressure phase of CaB6 has ductile behaviors, and its ductility increases with the increase of pressure. On the contrary, the calculated results indicate that the low pressure phase of CaB6 is brittle. The calculated Debye temperature indicates that the thermal conductivity of CaB6 is not very good. Furthermore, based on the Christoffel equation, the slowness surface of the acoustic waves is obtained.

关键词： density-functional theory elastic properties pressure effects acoustic properties

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

First-Principles Studies of Structural Evolutions in Cathode Materials LiMO_(2)(M=Co,Mn,Ni)

引用

Chinese Physics Letters 2024年第10期41卷 129-136页

作者： Yufeng Sun Xin-Gao Gong Ji-Hui Yang key laboratory for computational physical sciences(moe) Department of PhysicsFudan UniversityShanghai 200433China Shanghai Qizhi Institution Shanghai 200232China

We explore the structural evolutions of stoichiometric LiMO_(2)using the first-principles calculations combined with the cluster expansion *** automatically obtain the ground state structures of the stoichiometric LiMO_(2)by just considering the cation orderings in the quasi rock-salt structures and the following structural relaxations due to both the atomic size mismatches and the Jahn–Teller *** point out that,on the one hand,the cation orderings are mainly determined by the nearest,the second nearest,and the third nearest cation interactions and can be obtained from the‘phase diagram’we have built using the relative strengths of effective cluster interaction(ECI).On the other hand,the structural relaxations are dominated by the crystal field splitting(CFS)energies,i.e.,structures with larger CFS energies are more *** calculating the ECIs and CFS energies for various structures of LiMO_(2),we clearly show how ECI and CFS play roles in determining the structural evolution mechanism of these systems.

关键词： method relaxation cluster

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

Amyloid-β peptide aggregation and the influence of carbon nanoparticles

引用

Chinese Physics B 2016年第1期25卷 324-332页

作者：郗文辉韦广红 key laboratory for computational physical sciences (Ministry of Education) State Key Laboratory of Surface PhysicsDepartment of Physics Fudan University

Soluble peptides or proteins can self-aggregate into insoluble, ordered amyloid fibrils under appropriate conditions. These amyloid aggregates are the hallmarks of several human diseases ranging from neurodegenerative disorders to sys- temic amyloidoses. In this review, we first introduce the common structural features of amyloid fibrils and the amyloid fibrillation kinetics determined from experimental studies. Then, we discuss the structural models of Alzheimer＇s amyloid- β （Aβ） fibrils derived from solid-state nuclear magnetic resonance spectroscopy. On the computational side, molecular dynamics simulations can provide atomic details of structures and the underlying oligomerization mechanisms. We finally summarize recent progress in atomistic simulation studies on the oligomerization of β （including full-length Af and its fragments） and the influence of carbon nanoparticles.

关键词： Amyloid-β oligomerization carbon nanoparticles molecular dynamics

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

Recent advances in protein conformation sampling by combining machine learning with molecular simulation

引用

Chinese Physics B 2024年第3期33卷 80-87页

作者：唐一鸣杨中元姚逸飞周运谈圆王子超潘瞳熊瑞孙俊力韦广红 Department of Physics State Key Laboratory of Surface Physicsand Key Laboratory for Computational Physical Sciences (Ministry of Education)Shanghai 200438China

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational *** of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large *** review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational *** first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy ***,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein ***,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann ***,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

关键词： machine learning molecular simulation protein conformational space enhanced sampling

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

欢迎您,

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

请选择保存的检索档案：

请选择收藏分类：

通借通还

欢迎您,

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：