The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into...The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.展开更多
Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the ...Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.展开更多
It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we p...It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we present an analysis of the evolutionary history of a putative de novo gene,lawc,which overlaps with the conserved Trf2 gene,which encodes a general transcription factor in Drosophila melanogaster.We demonstrate that lawc emerged approximately 68 million years ago in the 5'-untranslated region(UTR)of Trf2 and displays an extensive spatiotemporal expression pattern.One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short,highly conserved regions located in Trf2 introns.This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes.The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2.This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.展开更多
The development of a general discrete element method for irregularly shaped particles is the core issue of the simulation of the dynamic behavior of granular materials.The general energy-conserving contact theory is u...The development of a general discrete element method for irregularly shaped particles is the core issue of the simulation of the dynamic behavior of granular materials.The general energy-conserving contact theory is used to establish a universal discrete element method suitable for particle contact of arbitrary shape.In this study,three dimentional(3D)modeling and scanning techniques are used to obtain a triangular mesh representation of the true particles containing typical concave particles.The contact volumebased energy-conserving model is used to realize the contact detection between irregularly shaped particles,and the contact force model is refined and modified to describe the contact under real conditions.The inelastic collision processes between the particles and boundaries are simulated to verify the robustness of the modified contact force model and its applicability to the multi-point contact mode.In addition,the packing process and the flow process of a large number of irregular particles are simulated with the modified discrete element method(DEM)to illustrate the applicability of the method of complex problems.展开更多
Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. Howeve...Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.展开更多
This paper discusses the k-degree averaging discontinuous finite element solution for the initial value problem of ordinary differential equations. When k is even, the averaging numerical flux （the average of left an...This paper discusses the k-degree averaging discontinuous finite element solution for the initial value problem of ordinary differential equations. When k is even, the averaging numerical flux （the average of left and right limits for the discontinuous finite element at nodes） has the optimal-order ultraconvergence 2k ＋ 2. For nanlinear Hamiltonian systems （e.g., SchrSdinger equation and Kepler system） with momentum conservation, the discontinuous finite element methods preserve momentum at nodes. These properties are confirmed by numerical experiments.展开更多
Energy conservation of nonlinear Schrodinger ordinary differential equation was proved through using continuous finite element methods of ordinary differential equation; Energy integration conservation was proved thro...Energy conservation of nonlinear Schrodinger ordinary differential equation was proved through using continuous finite element methods of ordinary differential equation; Energy integration conservation was proved through using space-time continuous fully discrete finite element methods and the electron nearly conservation with higher order error was obtained through using time discontinuous only space continuous finite element methods of nonlinear Schrodinger partial equation. The numerical results are in accordance with the theory.展开更多
The hierarchical reconstruction （HR） [Liu, Shu, Tadmor and Zhang, SINUM ＇07] has been successfully applied to prevent oscillations in solutions computed by finite volume, Runge-Kutta discontinuous Galerkin, spectra...The hierarchical reconstruction （HR） [Liu, Shu, Tadmor and Zhang, SINUM ＇07] has been successfully applied to prevent oscillations in solutions computed by finite volume, Runge-Kutta discontinuous Galerkin, spectral volume schemes for solving hyperbolic conservation laws. In this paper, we demonstrate that HR can also be combined with spectral/hp element method for solving hyperbolic conservation laws. An orthogonal spectral basis written in terms of Jacobi polynomials is applied. High computational efficiency is obtained due to such matrix-free algorithm. The formulation is conservative, and essential nomoscillation is enforced by the HR limiter. We show that HR preserves the order of accuracy of the spectral/hp element method for smooth solution problems and generate essentially non-oscillatory solutions profiles for capturing discontinuous solutions without local characteristic decomposition. In addition, we introduce a postprocessing technique to improve HR for limiting high degree numerical solutions.展开更多
In this paper we propose a spectral element: vanishing viscosity (SEW) method for the conservation laws on the semi-infinite interval. By using a suitable mapping, the problem is first transformed into a modified cons...In this paper we propose a spectral element: vanishing viscosity (SEW) method for the conservation laws on the semi-infinite interval. By using a suitable mapping, the problem is first transformed into a modified conservation law in a bounded interval, then the well-known spectral vanishing viscosity technique is generalized to the multi-domain case in order to approximate this trarsformed equation more efficiently. The construction details and convergence analysis are presented. Under a usual assumption of boundedness of the approximation solutions, it is proven that the solution of the SEW approximation converges to the uniciue entropy solution of the conservation laws. A number of numerical tests is carried out to confirm the theoretical results.展开更多
Conserved non-coding sequences(CNSs)are integral elements of transcriptional regulation.Transcriptional tuning of PLETHORA(PLT)genes that encode master regulators of plant development is vital for embryogenesis and me...Conserved non-coding sequences(CNSs)are integral elements of transcriptional regulation.Transcriptional tuning of PLETHORA(PLT)genes that encode master regulators of plant development is vital for embryogenesis and meristematic function.However,how the expression of PLT genes is modulated through CNSs remains unclear.Through motif-based mining of upstream sequences in 120 angiosperm ge-nomes,we identified 21 conserved and lineage-specific CNSs,two of which are unusually long,similar,and colinear within eudicots.Using Arabidopsis thaliana,we demonstrate that these two deeply conserved elements,which we named BOX1 and BOX2,control PLT1 and PLT2 expression.CRISPR mutants within these elements specifically reduced PLT expression levels,and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip,affecting the abil-ity to rescue the plt1 plt2 double mutant.We further show that the influence of these elements on expres-sion patterns is already exerted during embryogenesis and functional in the context of the early embryo.Finally,we reveal the existence of a BOX-mediated autoregulatory feedback loop that,in large part,explains CNS influence on expression patterns.Wethus uncover a transcriptional mechanism by which genes encoding master regulators of embryo and root meristem development are regulated.展开更多
Element Transfer Reaction(ETR)theory is a new fundamental theory guiding the design of synthetic routes.It analyses problems from a brand-new perspective of element circulation,decomposing the factors affecting synthe...Element Transfer Reaction(ETR)theory is a new fundamental theory guiding the design of synthetic routes.It analyses problems from a brand-new perspective of element circulation,decomposing the factors affecting synthetic efficiency into three elements:element sources,driving force,and output.Different from the retrosynthetic analysis method and the atom economy theory,the ETR theory places more emphasis on examining the problem as a whole and comprehensively considering various factors involved in industrial applications.This perspective intends to elaborate on the scientific connotation of the ETR theory and explore its characteristics by discussing the practical application cases.展开更多
In this paper,a composite numerical scheme is proposed to solve the threedimensional Darcy-Forchheimer miscible displacement problem with positive semi-definite assumptions.A mixed finite element is used for the fow e...In this paper,a composite numerical scheme is proposed to solve the threedimensional Darcy-Forchheimer miscible displacement problem with positive semi-definite assumptions.A mixed finite element is used for the fow equation.The velocity and pressure are computed simultaneously.The accuracy of velocity is improved one order.The concentration equation is solved by using mixed finite element,multi-step difference and upwind approximation.A multi-step method is used to approximate time derivative for improving the accuracy.The upwind approximation and an expanded mixed finite element are adopted to solve the convection and diffusion,respectively.The composite method could compute the diffusion flux and its gradient.It possibly becomes an eficient tool for solving convection-dominated diffusion problems.Firstly,the conservation of mass holds.Secondly,the multi-step method has high accuracy.Thirdly,the upwind approximation could avoid numerical dispersion.Using numerical analysis of a priori estimates and special techniques of differential equations,we give an error estimates for a positive definite problem.Numerical experiments illustrate its computational efficiency and feasibility of application.展开更多
The floristic elements and the geographical distribution are analyzed in thispaper based on statistics of elements of rare and endangered plants in Tibet. The results have beengained as following: (1) According to ...The floristic elements and the geographical distribution are analyzed in thispaper based on statistics of elements of rare and endangered plants in Tibet. The results have beengained as following: (1) According to 'the National Important Wild Conservative Plants List (List1)' and 'the National Important Wild Conservative Plants List (List 1)', there are a total of 54plant species (48 genera and 33 families); (2) The geographical elements are very complicated inTibet with 12 of 15 distribution patterns of genera classified by academician Wu; (3) There areobvious temperate genera with 28 genera accounting for 60. 4% of the total genera; (4) There areabundant endemic species accounting for 18. 52% of total species but poor endemic genera; (5) Thegeographical distribution is uneven and a great of species distribute in the areas between 1 000 mand 3 500 m above sea level; (6) To protect the rare and endangered plants efficiently, sixconservation measures are proposed, and 35 species are suggested for the conservative plants of theautonomous conservation level.展开更多
Induction and mobilization of transposable elements （TEs） following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associa...Induction and mobilization of transposable elements （TEs） following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs （IncRNAs）, many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and IncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild- type （WT） and ataxia telangiectasia mutated （atm） mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is 〉 2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cy- cle is largely lost. In contrast, only less than 0.6% of TEs and IncRNAs respond to DNA damage in WT plants, and the regulation of 〉95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and IncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and IncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and IncRNAs located close to genes commonly function as controlling elements.展开更多
This paper addresses the conservation laws in finite brittle solids with microcracks. The discussion is limited to the 2-D cases. First, after considering the combination of the Pseudo-Traction Method and the indirect...This paper addresses the conservation laws in finite brittle solids with microcracks. The discussion is limited to the 2-D cases. First, after considering the combination of the Pseudo-Traction Method and the indirect Boundary Element Method, a versatile method for solving multi-crack interacting problems in finite plane solids is proposed, by which the fracture parameters （SIF and path-independent integrals） can be calculated with a desirable accuracy. Second, with the aid of the method proposed, the roles the conservation laws play in the fracture analysis for finite microcracking solids are studied. It is concluded that the conservation laws do play important roles in not only the fracture analysis but also the analysis of damage and stability for the finite microcracking system. Finally, the physical interpretation of the M-integral is discussed further. An explicit relation between the M-integral and the crack face area, i.e., M = GS, has been discovered using the analytical method, which can shed some light on the Damage Mechanics issues from a different perspective.展开更多
By applying the continuous finite element methods of ordinary differential equations, the linear element methods are proved having second-order pseudo-symplectic scheme and the quadratic element methods are proved hav...By applying the continuous finite element methods of ordinary differential equations, the linear element methods are proved having second-order pseudo-symplectic scheme and the quadratic element methods are proved having third-order pseudo- symplectic scheme respectively for general Hamiltonian systems, and they both keep energy conservative. The finite element methods are proved to be symplectic as well as energy conservative for linear Hamiltonian systems. The numerical results are in agree-ment with theory.展开更多
Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and...Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).展开更多
The physical model is described by a seepage coupled system for simulating numerically three-dimensional chemical oil recovery, whose mathematical description includes three equations to interpret main concepts. The p...The physical model is described by a seepage coupled system for simulating numerically three-dimensional chemical oil recovery, whose mathematical description includes three equations to interpret main concepts. The pressure equation is a nonlinear parabolic equation, the concentration is defined by a convection-diffusion equation and the saturations of different components are stated by nonlinear convection-diffusion equations. The transport pressure appears in the concentration equation and saturation equations in the form of Darcy velocity, and controls their processes. The flow equation is solved by the conservative mixed volume element and the accuracy is improved one order for approximating Darcy velocity. The method of characteristic mixed volume element is applied to solve the concentration, where the diffusion is discretized by a mixed volume element method and the convection is treated by the method of characteristics. The characteristics can confirm strong computational stability at sharp fronts and it can avoid numerical dispersion and nonphysical oscillation. The scheme can adopt a large step while its numerical results have small time-truncation error and high order of accuracy. The mixed volume element method has the law of conservation on every element for the diffusion and it can obtain numerical solutions of the concentration and adjoint vectors. It is most important in numerical simulation to ensure the physical conservative nature. The saturation different components are obtained by the method of characteristic fractional step difference. The computational work is shortened greatly by decomposing a three-dimensional problem into three successive one-dimensional problems and it is completed easily by using the algorithm of speedup. Using the theory and technique of a priori estimates of differential equations, we derive an optimal second order estimates in 12 norm. Numerical examples are given to show the effectiveness and practicability and the method is testified as a powerful tool to solve the important problems.展开更多
We derived and analyzed a new numerical scheme for the coupled Stokes and Darcy problems by using H（div） conforming elements in the entire domain. The approach employs the mixed finite element method for the Darcy e...We derived and analyzed a new numerical scheme for the coupled Stokes and Darcy problems by using H（div） conforming elements in the entire domain. The approach employs the mixed finite element method for the Darcy equations and a stabilized H（div） finite element method for the Stokes equations. Optimal error estimates for the fluid velocity and pressure are derived. The finite element solutions from the new scheme not only feature a full satisfaction of the continuity equation, which is highly demanded in scientific computing, but also satisfy the mass conservation.展开更多
The scientific community faces the challenge of measuring progress toward biodiversity targets and indices have been traditionally used.However,recent inventories in secondary tropical mountain forests using tradition...The scientific community faces the challenge of measuring progress toward biodiversity targets and indices have been traditionally used.However,recent inventories in secondary tropical mountain forests using traditional biodiversity indices have yielded results that are indistinct with primary ones.This shows the need to develop complementary indices that goes beyond species count but integrates the distribution and conservation status of the species.This study developed endemicity and conservation importance index for tropical forest that incorporated the distribution and conservation status of the species.These indices were applied to Mt.Natoo,a remnant primary mossy forest in Buguias,Benguet,Philippines,that resulted to endemicity index of 81.07 and conservation importance index of 42.90.Comparing these with secondary forest sites with comparable Shannon-Wiener,Simpson,Evenness and Margalef’s indices,our endemicity and conservation indices clearly differentiates primary forest(our study site)with higher values from secondary forests with much lower values.Thus,we are proposing these indices for a direct but scientifically-informed identification of specific sites for conservation and protection in tropical forests.Additionally,our study documented a total of 168 vascular plant species(79 endemic and 12 locally threatened species)in Mt.Nato-o.Majority are of tropical elements for both generic and species levels with some temperate elements that could be attributed to the site's high elevation and semi-temperate climate.These are important baseline information for conservation plans and monitoring of tropical mossy forests.展开更多
基金supported by the National Key R&D Program of China(Grant No.2020YFA0712402)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDPB17)+3 种基金the CAS Project for Young Scientists in Basic Research(Grant No.YSBR-077)the National Natural Science Foundation of China(Grant Nos.12025107,11871463,11688101,and 61621003)the National Thousand Youth Talents Plan,and the CAS“Light of West China”Program(Grant No.xbzg-zdsys-201913)China.We thank High Performance Computing(HPC)of Northwest A&F University(NWAFU)for providing computing resources。
文摘The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.
基金supported by the National Natural Science Foundation of China(grant number:31571361).
文摘Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.
基金funded by a grant from the Russian Science Foundation № 24-24-00354
文摘It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we present an analysis of the evolutionary history of a putative de novo gene,lawc,which overlaps with the conserved Trf2 gene,which encodes a general transcription factor in Drosophila melanogaster.We demonstrate that lawc emerged approximately 68 million years ago in the 5'-untranslated region(UTR)of Trf2 and displays an extensive spatiotemporal expression pattern.One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short,highly conserved regions located in Trf2 introns.This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes.The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2.This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.
基金supported by the National Key Research and Development Program of China(2018YFA0605902)the National Natural Science Foundation of China(42176241 and 11872136).
文摘The development of a general discrete element method for irregularly shaped particles is the core issue of the simulation of the dynamic behavior of granular materials.The general energy-conserving contact theory is used to establish a universal discrete element method suitable for particle contact of arbitrary shape.In this study,three dimentional(3D)modeling and scanning techniques are used to obtain a triangular mesh representation of the true particles containing typical concave particles.The contact volumebased energy-conserving model is used to realize the contact detection between irregularly shaped particles,and the contact force model is refined and modified to describe the contact under real conditions.The inelastic collision processes between the particles and boundaries are simulated to verify the robustness of the modified contact force model and its applicability to the multi-point contact mode.In addition,the packing process and the flow process of a large number of irregular particles are simulated with the modified discrete element method(DEM)to illustrate the applicability of the method of complex problems.
文摘Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.
基金Project supported by the National Natural Science Foundation of China (No. 10771063)
文摘This paper discusses the k-degree averaging discontinuous finite element solution for the initial value problem of ordinary differential equations. When k is even, the averaging numerical flux （the average of left and right limits for the discontinuous finite element at nodes） has the optimal-order ultraconvergence 2k ＋ 2. For nanlinear Hamiltonian systems （e.g., SchrSdinger equation and Kepler system） with momentum conservation, the discontinuous finite element methods preserve momentum at nodes. These properties are confirmed by numerical experiments.
基金Project supported by the National Basic Research Program of China (973 program) (No.G1999032804)
文摘Energy conservation of nonlinear Schrodinger ordinary differential equation was proved through using continuous finite element methods of ordinary differential equation; Energy integration conservation was proved through using space-time continuous fully discrete finite element methods and the electron nearly conservation with higher order error was obtained through using time discontinuous only space continuous finite element methods of nonlinear Schrodinger partial equation. The numerical results are in accordance with the theory.
基金Research was supported in part by NSF grant DMS-0800612Research was supported by Applied Mathematics program of the US DOE Office of Advanced Scientific Computing ResearchThe Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830
文摘The hierarchical reconstruction （HR） [Liu, Shu, Tadmor and Zhang, SINUM ＇07] has been successfully applied to prevent oscillations in solutions computed by finite volume, Runge-Kutta discontinuous Galerkin, spectral volume schemes for solving hyperbolic conservation laws. In this paper, we demonstrate that HR can also be combined with spectral/hp element method for solving hyperbolic conservation laws. An orthogonal spectral basis written in terms of Jacobi polynomials is applied. High computational efficiency is obtained due to such matrix-free algorithm. The formulation is conservative, and essential nomoscillation is enforced by the HR limiter. We show that HR preserves the order of accuracy of the spectral/hp element method for smooth solution problems and generate essentially non-oscillatory solutions profiles for capturing discontinuous solutions without local characteristic decomposition. In addition, we introduce a postprocessing technique to improve HR for limiting high degree numerical solutions.
文摘In this paper we propose a spectral element: vanishing viscosity (SEW) method for the conservation laws on the semi-infinite interval. By using a suitable mapping, the problem is first transformed into a modified conservation law in a bounded interval, then the well-known spectral vanishing viscosity technique is generalized to the multi-domain case in order to approximate this trarsformed equation more efficiently. The construction details and convergence analysis are presented. Under a usual assumption of boundedness of the approximation solutions, it is proven that the solution of the SEW approximation converges to the uniciue entropy solution of the conservation laws. A number of numerical tests is carried out to confirm the theoretical results.
基金funded by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek(GSGT.2019.019 to M.K.)supported by the Office of Science of the US Department of Energy(Contract No.DE-AC02-05CH11231).
文摘Conserved non-coding sequences(CNSs)are integral elements of transcriptional regulation.Transcriptional tuning of PLETHORA(PLT)genes that encode master regulators of plant development is vital for embryogenesis and meristematic function.However,how the expression of PLT genes is modulated through CNSs remains unclear.Through motif-based mining of upstream sequences in 120 angiosperm ge-nomes,we identified 21 conserved and lineage-specific CNSs,two of which are unusually long,similar,and colinear within eudicots.Using Arabidopsis thaliana,we demonstrate that these two deeply conserved elements,which we named BOX1 and BOX2,control PLT1 and PLT2 expression.CRISPR mutants within these elements specifically reduced PLT expression levels,and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip,affecting the abil-ity to rescue the plt1 plt2 double mutant.We further show that the influence of these elements on expres-sion patterns is already exerted during embryogenesis and functional in the context of the early embryo.Finally,we reveal the existence of a BOX-mediated autoregulatory feedback loop that,in large part,explains CNS influence on expression patterns.Wethus uncover a transcriptional mechanism by which genes encoding master regulators of embryo and root meristem development are regulated.
基金Industry Foresight and Key Core Technology(No.YZ2023019)Cooperation Project of Yangzhou City with Yangzhou University(No.YZ2023209)+3 种基金Sichuan Tianfu Talent Programme(No.A.2200732)Chengdu Rongpiao Talent Programme(No.1043)SeleValley Scholars Basic Research Project(No.2301)Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)for financial support。
文摘Element Transfer Reaction(ETR)theory is a new fundamental theory guiding the design of synthetic routes.It analyses problems from a brand-new perspective of element circulation,decomposing the factors affecting synthetic efficiency into three elements:element sources,driving force,and output.Different from the retrosynthetic analysis method and the atom economy theory,the ETR theory places more emphasis on examining the problem as a whole and comprehensively considering various factors involved in industrial applications.This perspective intends to elaborate on the scientific connotation of the ETR theory and explore its characteristics by discussing the practical application cases.
基金supported by the Natural Science Foundation of Shandong Province(ZR2021MA019)the National Natural Science Foundation of China(11871312)。
文摘In this paper,a composite numerical scheme is proposed to solve the threedimensional Darcy-Forchheimer miscible displacement problem with positive semi-definite assumptions.A mixed finite element is used for the fow equation.The velocity and pressure are computed simultaneously.The accuracy of velocity is improved one order.The concentration equation is solved by using mixed finite element,multi-step difference and upwind approximation.A multi-step method is used to approximate time derivative for improving the accuracy.The upwind approximation and an expanded mixed finite element are adopted to solve the convection and diffusion,respectively.The composite method could compute the diffusion flux and its gradient.It possibly becomes an eficient tool for solving convection-dominated diffusion problems.Firstly,the conservation of mass holds.Secondly,the multi-step method has high accuracy.Thirdly,the upwind approximation could avoid numerical dispersion.Using numerical analysis of a priori estimates and special techniques of differential equations,we give an error estimates for a positive definite problem.Numerical experiments illustrate its computational efficiency and feasibility of application.
文摘The floristic elements and the geographical distribution are analyzed in thispaper based on statistics of elements of rare and endangered plants in Tibet. The results have beengained as following: (1) According to 'the National Important Wild Conservative Plants List (List1)' and 'the National Important Wild Conservative Plants List (List 1)', there are a total of 54plant species (48 genera and 33 families); (2) The geographical elements are very complicated inTibet with 12 of 15 distribution patterns of genera classified by academician Wu; (3) There areobvious temperate genera with 28 genera accounting for 60. 4% of the total genera; (4) There areabundant endemic species accounting for 18. 52% of total species but poor endemic genera; (5) Thegeographical distribution is uneven and a great of species distribute in the areas between 1 000 mand 3 500 m above sea level; (6) To protect the rare and endangered plants efficiently, sixconservation measures are proposed, and 35 species are suggested for the conservative plants of theautonomous conservation level.
文摘Induction and mobilization of transposable elements （TEs） following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs （IncRNAs）, many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and IncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild- type （WT） and ataxia telangiectasia mutated （atm） mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is 〉 2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cy- cle is largely lost. In contrast, only less than 0.6% of TEs and IncRNAs respond to DNA damage in WT plants, and the regulation of 〉95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and IncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and IncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and IncRNAs located close to genes commonly function as controlling elements.
基金Project supported by the National Natural Science Foundation of China (No. 19472053).
文摘This paper addresses the conservation laws in finite brittle solids with microcracks. The discussion is limited to the 2-D cases. First, after considering the combination of the Pseudo-Traction Method and the indirect Boundary Element Method, a versatile method for solving multi-crack interacting problems in finite plane solids is proposed, by which the fracture parameters （SIF and path-independent integrals） can be calculated with a desirable accuracy. Second, with the aid of the method proposed, the roles the conservation laws play in the fracture analysis for finite microcracking solids are studied. It is concluded that the conservation laws do play important roles in not only the fracture analysis but also the analysis of damage and stability for the finite microcracking system. Finally, the physical interpretation of the M-integral is discussed further. An explicit relation between the M-integral and the crack face area, i.e., M = GS, has been discovered using the analytical method, which can shed some light on the Damage Mechanics issues from a different perspective.
基金Project supported by the National Natural Science Foundation of China (No.10471038)
文摘By applying the continuous finite element methods of ordinary differential equations, the linear element methods are proved having second-order pseudo-symplectic scheme and the quadratic element methods are proved having third-order pseudo- symplectic scheme respectively for general Hamiltonian systems, and they both keep energy conservative. The finite element methods are proved to be symplectic as well as energy conservative for linear Hamiltonian systems. The numerical results are in agree-ment with theory.
基金ZokorDB is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB13000000)The authors are also supported by the National Natural Science Foundation of China(NSFC)(Nos.11871463,11871462,61671444 and 61621003)+1 种基金We thank all the lab members for discussions on data collection,genome alignment,annotation,GRN reconstructionWe thank Dr.Yilei Wu and his group for help on database design and management.
文摘Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).
基金Supported by the National Natural Science Foundation of China(11101124 and 11271231)Natural Science Foundation of Shandong Province(ZR2016AM08)National Tackling Key Problems Program(2011ZX05052,2011ZX05011-004)
文摘The physical model is described by a seepage coupled system for simulating numerically three-dimensional chemical oil recovery, whose mathematical description includes three equations to interpret main concepts. The pressure equation is a nonlinear parabolic equation, the concentration is defined by a convection-diffusion equation and the saturations of different components are stated by nonlinear convection-diffusion equations. The transport pressure appears in the concentration equation and saturation equations in the form of Darcy velocity, and controls their processes. The flow equation is solved by the conservative mixed volume element and the accuracy is improved one order for approximating Darcy velocity. The method of characteristic mixed volume element is applied to solve the concentration, where the diffusion is discretized by a mixed volume element method and the convection is treated by the method of characteristics. The characteristics can confirm strong computational stability at sharp fronts and it can avoid numerical dispersion and nonphysical oscillation. The scheme can adopt a large step while its numerical results have small time-truncation error and high order of accuracy. The mixed volume element method has the law of conservation on every element for the diffusion and it can obtain numerical solutions of the concentration and adjoint vectors. It is most important in numerical simulation to ensure the physical conservative nature. The saturation different components are obtained by the method of characteristic fractional step difference. The computational work is shortened greatly by decomposing a three-dimensional problem into three successive one-dimensional problems and it is completed easily by using the algorithm of speedup. Using the theory and technique of a priori estimates of differential equations, we derive an optimal second order estimates in 12 norm. Numerical examples are given to show the effectiveness and practicability and the method is testified as a powerful tool to solve the important problems.
基金The Key Technologies R&D Program ofSichuan Province (No.05GG006-0062)
文摘We derived and analyzed a new numerical scheme for the coupled Stokes and Darcy problems by using H（div） conforming elements in the entire domain. The approach employs the mixed finite element method for the Darcy equations and a stabilized H（div） finite element method for the Stokes equations. Optimal error estimates for the fluid velocity and pressure are derived. The finite element solutions from the new scheme not only feature a full satisfaction of the continuity equation, which is highly demanded in scientific computing, but also satisfy the mass conservation.
文摘The scientific community faces the challenge of measuring progress toward biodiversity targets and indices have been traditionally used.However,recent inventories in secondary tropical mountain forests using traditional biodiversity indices have yielded results that are indistinct with primary ones.This shows the need to develop complementary indices that goes beyond species count but integrates the distribution and conservation status of the species.This study developed endemicity and conservation importance index for tropical forest that incorporated the distribution and conservation status of the species.These indices were applied to Mt.Natoo,a remnant primary mossy forest in Buguias,Benguet,Philippines,that resulted to endemicity index of 81.07 and conservation importance index of 42.90.Comparing these with secondary forest sites with comparable Shannon-Wiener,Simpson,Evenness and Margalef’s indices,our endemicity and conservation indices clearly differentiates primary forest(our study site)with higher values from secondary forests with much lower values.Thus,we are proposing these indices for a direct but scientifically-informed identification of specific sites for conservation and protection in tropical forests.Additionally,our study documented a total of 168 vascular plant species(79 endemic and 12 locally threatened species)in Mt.Nato-o.Majority are of tropical elements for both generic and species levels with some temperate elements that could be attributed to the site's high elevation and semi-temperate climate.These are important baseline information for conservation plans and monitoring of tropical mossy forests.
