The electronic and topological properties of FeGe2 with a tetragonal crystal structure were investigated via first-principles calculations.The results demonstrate that FeGe2 in this structure exhibits anti-ferromagnet...The electronic and topological properties of FeGe2 with a tetragonal crystal structure were investigated via first-principles calculations.The results demonstrate that FeGe2 in this structure exhibits anti-ferromagnetism,with two bands crossing the Fermi level nesting each other at high-symmetry points in the Brillouin zone,forming a nodal ring where the nodes intersect in momentum space.Additionally,it possesses nontrivial topological surface states.Upon inclusion of SOC(spin-orbit coupling),there are no significant changes observed in the band structure,nodal features,or surface states,indicating the persistence of its topological nodal-line characteristics.展开更多
Superconducting transition temperature(Tc),as a crucial parameter,exploring its relationship with various macroscopic and microscopic factors helps to understand the mechanism of high-temperature superconductivity fro...Superconducting transition temperature(Tc),as a crucial parameter,exploring its relationship with various macroscopic and microscopic factors helps to understand the mechanism of high-temperature superconductivity from multiple perspectives,aiding in a multidimensional comprehension of high-temperature superconductivity mechanisms.Drawing inspiration from the block-layer structure models of cuprate superconductors,we computationally investigated the interlayer interaction energies in the 12442-type iron-based superconducting materials AkCa_(2)Fe_(4)As_(4)F_(2)(Ak=K,Rb,Cs)systems based on the block-layer model and explored their relationship with Tc.We observed that an increase in interlayer combinative energy leads to a decrease in Tc,while conversely,a decrease in interlayer combination energy results in an increase in Tc.Further,we found that the contribution of the Fe 3d band structure,especially the 3dz2 orbital,to charge transfer is significant.展开更多
In this study,we performed first-principles calculations using the VASP(Vienna Ab initio Simulation)software package to investigate the crystal structure,electronic structure,and optical properties of a new layered te...In this study,we performed first-principles calculations using the VASP(Vienna Ab initio Simulation)software package to investigate the crystal structure,electronic structure,and optical properties of a new layered ternary metal chalcogenide,Eu_(2)InTe_(5).Our results show that Eu_(2)InTe_(5) is a non-zero-gap metal with a layered structure characterized by strong intra-layer atomic bonding and weak inter-layer interaction,which suggests its potential application as a nanomaterial.We also studied the optical properties,including the absorption coefficient,imaginary and real parts of the complex dielectric constant,and found that Eu_(2)InTe_(5) exhibits strong photoresponse characteristics at the junction of ultraviolet and visible light as well as blue-green light,with peaks at wavelengths of 389 nm and 477 nm.This suggests that it could be used in the development of UV(ultraviolet)detectors and other optoelectronic devices.Furthermore,due to its strong absorption,low loss,and low reflectivity,Eu_(2)InTe_(5) has the potential to be used as a promising photovoltaic absorption layer in solar cells.展开更多
In the last decade,RNA-sequencing(RNA-seq)has surpassed microarray to become the gold standard for gene expression profiling due to the continuous drop in sequencing cost and the latest development of easy-to-use libr...In the last decade,RNA-sequencing(RNA-seq)has surpassed microarray to become the gold standard for gene expression profiling due to the continuous drop in sequencing cost and the latest development of easy-to-use library construction kits.To date,the Arabidopsis community has collectively released more than 20000 RNA-seq libraries,with over 1300 libraries deposited just in the first quarter of 2019(Figure 1A).This vast resource is tremendously useful for all Arabidopsis researchers to study transcriptional regulation,tissue specificity,stress responses,and developmental dynamics of genes in which they are interested.展开更多
Precise mapping of quantitative trait loci(QTLs)is critical for assessing genetic effects and identifying candidate genes for quantitative traits.Interval and composite interval mappings have been the methods of choic...Precise mapping of quantitative trait loci(QTLs)is critical for assessing genetic effects and identifying candidate genes for quantitative traits.Interval and composite interval mappings have been the methods of choice for several decades,which have provided tools for identifying genomic regions harboring causal genes for quantitative traits.Historically,the concept was developed on the basis of sparse marker maps where genotypes of loci within intervals could not be observed.Currently,genomes of many organisms have been saturated with markers due to the new sequencing technologies.Genotyping by sequencing usually generates hundreds of thousands of single nucleotide polymorphisms(SNPs),which often include the causal polymorphisms.The concept of interval no longer exists,prompting the necessity of a norm change in QTL mapping technology to make use of the high-volume genomic data.Here we developed a statistical method and a software package to map QTLs by binning markers into haplotype blocks,called bins.The new method detects associations of bins with quantitative traits.It borrows the mixed model methodology with a polygenic control from genome-wide association studies(GWAS)and can handle all kinds of experimental populations under the linear mixed model(LMM)framework.We tested the method using both simulated data and data from populations of rice.The results showed that this method has higher power than the current methods.An R package named binQTL is available from GitHub.展开更多
Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.Currently,there is no specialized graphical user interface(GUI)designed to produce non-circular whole genom...Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.Currently,there is no specialized graphical user interface(GUI)designed to produce non-circular whole genome diagrams,and the use of existing tools requires considerable coding effort from users.Moreover,such tools also require improvement,including the addition of new functionalities.To address these issues,we developed a new R/Shiny application,named shiny Chromosome,as a GUI for the interactive creation of non-circular whole genome diagrams.shiny Chromosome can be easily installed on personal computers for own use as well as on local or public servers for community use.Publication-quality images can be readily generated and annotated from user input using diverse widgets.shiny Chromosome is deployed at http://150.109.59.144:3838/shiny Chromosome/,http://shiny Chromosome.ncpgr.cn,and https://yimingyu.shinyapps.io/shiny Chromosome for online use.The source code and manual of shiny Chromosome are freely available at https://github.com/venyao/shiny Chromosome.展开更多
文摘The electronic and topological properties of FeGe2 with a tetragonal crystal structure were investigated via first-principles calculations.The results demonstrate that FeGe2 in this structure exhibits anti-ferromagnetism,with two bands crossing the Fermi level nesting each other at high-symmetry points in the Brillouin zone,forming a nodal ring where the nodes intersect in momentum space.Additionally,it possesses nontrivial topological surface states.Upon inclusion of SOC(spin-orbit coupling),there are no significant changes observed in the band structure,nodal features,or surface states,indicating the persistence of its topological nodal-line characteristics.
文摘Superconducting transition temperature(Tc),as a crucial parameter,exploring its relationship with various macroscopic and microscopic factors helps to understand the mechanism of high-temperature superconductivity from multiple perspectives,aiding in a multidimensional comprehension of high-temperature superconductivity mechanisms.Drawing inspiration from the block-layer structure models of cuprate superconductors,we computationally investigated the interlayer interaction energies in the 12442-type iron-based superconducting materials AkCa_(2)Fe_(4)As_(4)F_(2)(Ak=K,Rb,Cs)systems based on the block-layer model and explored their relationship with Tc.We observed that an increase in interlayer combinative energy leads to a decrease in Tc,while conversely,a decrease in interlayer combination energy results in an increase in Tc.Further,we found that the contribution of the Fe 3d band structure,especially the 3dz2 orbital,to charge transfer is significant.
文摘In this study,we performed first-principles calculations using the VASP(Vienna Ab initio Simulation)software package to investigate the crystal structure,electronic structure,and optical properties of a new layered ternary metal chalcogenide,Eu_(2)InTe_(5).Our results show that Eu_(2)InTe_(5) is a non-zero-gap metal with a layered structure characterized by strong intra-layer atomic bonding and weak inter-layer interaction,which suggests its potential application as a nanomaterial.We also studied the optical properties,including the absorption coefficient,imaginary and real parts of the complex dielectric constant,and found that Eu_(2)InTe_(5) exhibits strong photoresponse characteristics at the junction of ultraviolet and visible light as well as blue-green light,with peaks at wavelengths of 389 nm and 477 nm.This suggests that it could be used in the development of UV(ultraviolet)detectors and other optoelectronic devices.Furthermore,due to its strong absorption,low loss,and low reflectivity,Eu_(2)InTe_(5) has the potential to be used as a promising photovoltaic absorption layer in solar cells.
基金supported by National Natural Science Foundation of China(31871234)the Program for Guangdong Introducing Innovative and Entrepreneurial Teams(2016ZT06S172)+1 种基金the Shenzhen Sci-Tech Fund(KYTDPT20181011104005)supported by the Center for Computational Science and Engineering at Southern University of Science and Technology.
文摘In the last decade,RNA-sequencing(RNA-seq)has surpassed microarray to become the gold standard for gene expression profiling due to the continuous drop in sequencing cost and the latest development of easy-to-use library construction kits.To date,the Arabidopsis community has collectively released more than 20000 RNA-seq libraries,with over 1300 libraries deposited just in the first quarter of 2019(Figure 1A).This vast resource is tremendously useful for all Arabidopsis researchers to study transcriptional regulation,tissue specificity,stress responses,and developmental dynamics of genes in which they are interested.
基金supported by the National Key Research and Development Program (2016YFD0100802)the National Science Foundation Collaborative Research grant (DBI-1458515)
文摘Precise mapping of quantitative trait loci(QTLs)is critical for assessing genetic effects and identifying candidate genes for quantitative traits.Interval and composite interval mappings have been the methods of choice for several decades,which have provided tools for identifying genomic regions harboring causal genes for quantitative traits.Historically,the concept was developed on the basis of sparse marker maps where genotypes of loci within intervals could not be observed.Currently,genomes of many organisms have been saturated with markers due to the new sequencing technologies.Genotyping by sequencing usually generates hundreds of thousands of single nucleotide polymorphisms(SNPs),which often include the causal polymorphisms.The concept of interval no longer exists,prompting the necessity of a norm change in QTL mapping technology to make use of the high-volume genomic data.Here we developed a statistical method and a software package to map QTLs by binning markers into haplotype blocks,called bins.The new method detects associations of bins with quantitative traits.It borrows the mixed model methodology with a polygenic control from genome-wide association studies(GWAS)and can handle all kinds of experimental populations under the linear mixed model(LMM)framework.We tested the method using both simulated data and data from populations of rice.The results showed that this method has higher power than the current methods.An R package named binQTL is available from GitHub.
基金the research start-up fund to topnotch talents of Henan Agricultural University(Grant No.30500581),China.
文摘Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.Currently,there is no specialized graphical user interface(GUI)designed to produce non-circular whole genome diagrams,and the use of existing tools requires considerable coding effort from users.Moreover,such tools also require improvement,including the addition of new functionalities.To address these issues,we developed a new R/Shiny application,named shiny Chromosome,as a GUI for the interactive creation of non-circular whole genome diagrams.shiny Chromosome can be easily installed on personal computers for own use as well as on local or public servers for community use.Publication-quality images can be readily generated and annotated from user input using diverse widgets.shiny Chromosome is deployed at http://150.109.59.144:3838/shiny Chromosome/,http://shiny Chromosome.ncpgr.cn,and https://yimingyu.shinyapps.io/shiny Chromosome for online use.The source code and manual of shiny Chromosome are freely available at https://github.com/venyao/shiny Chromosome.
