We present a simulation for the reconstruction of the rotational quantum state of linear molecules to retrieve the density matrix. An optimal approach in the sense of minimal error limit is proposed, in which a variab...We present a simulation for the reconstruction of the rotational quantum state of linear molecules to retrieve the density matrix. An optimal approach in the sense of minimal error limit is proposed, in which a variable set of angular frequency is properly chosen and the least square inversion is then applied. This approach of reconstruction from time-dependent molecular-axis angular distribution is proved adaptable for various object states, which has a good numerical stability independent of the selected rotational space.展开更多
We establish a reconstruction approach for the rotational quantum state of linear molecules possessing a magnetic manifold. Our approximate method contains an iteration with generalized matrix inverses, processing the...We establish a reconstruction approach for the rotational quantum state of linear molecules possessing a magnetic manifold. Our approximate method contains an iteration with generalized matrix inverses, processing the tomographic integral of the time-dependent molecular-axis distribution in a polar angle. As shown in a simulated example for an alignment state, the density matrix is determined in a high fidelity. An analytic tomographic formula is also derived for the symmetric top rotation. The state coherent in the quantum space of both the angular momentum and its magnetic projection can be approximately retrieved from the observable time-resolved solid-angle distribution of the molecular axis.展开更多
The state reconstruction problem is addressed for complex dynamical networks coupled with states and outputs respectively, in a noisy transmission channel. By using Lyapunov stability theory and H∞ performance, two s...The state reconstruction problem is addressed for complex dynamical networks coupled with states and outputs respectively, in a noisy transmission channel. By using Lyapunov stability theory and H∞ performance, two schemes of state reconstruction are proposed for the complex dynamical networks with the nodes coupled by states and outputs respectively, and the estimation errors are convergent to zeros with H∞ performance index. A numerical simulation demonstrates the effectiveness of the proposed observers.展开更多
Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of traits.The development of ancestral state reconstruction(ASR)me...Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of traits.The development of ancestral state reconstruction(ASR)methods has provided the tools to reconstruct trait evolution,which are widely used in fields like evolutionary biology,macroecology and paleontology.As there are different elements involved in those analyses,with different levels of uncertainty(i.e.relating to branch length estimation,trait coding,statistical framework,taxon sampling or software),the various combinations of these elements likely have a strong impact on the reconstruction of the evolution of traits,potentially leading to opposite conclusions.To assess the impact of these different elements in ASR,we performed a set of analyses,including all possible combinations of such elements and using the evolution of migratory behavior in Sylvia warblers as a case study,which was coded as a continuous or as a discrete character.Our results show that taxon sampling,character coding,tree shape,statistical framework and software all significantly affect ASR,both individually and in combination.Not all reconstructed tree nodes show discrepancies,but in the critical ones most pairwise comparisons between analyses lead to conflicting and unexpectedly antagonistic results(zero migration vs fully migratory),thus challenging interpretations of trait evolution.We propose some possible solutions to partly inform decisions,involving the method selection and the incorporation of biological or fossil evidence regarding how traits evolve,but our results demand serious rethinking about how the research community currently uses ASR.展开更多
Certain deterministic nonlinear systems may show chaotic behavior. We consider the motion of qualitative information and the practicalities of extracting a part from chaotic experimental data. Our approach based on a ...Certain deterministic nonlinear systems may show chaotic behavior. We consider the motion of qualitative information and the practicalities of extracting a part from chaotic experimental data. Our approach based on a theorem of Takens draws on the ideas from the generalized theory of information known as singular system analysis. We illustrate this technique by numerical data from the chaotic region of the chaotic experimental data. The method of the singular-value decomposition is used to calculate the eigenvalues of embedding space matrix. The corresponding concrete algorithm to calculate eigenvectors and to obtain the basis of embedding vector space is proposed in this paper. The projection on the orthogonal basis generated by eigenvectors of timeseries data and concrete paradigm are also provided here. Meanwhile the state space reconstruction technology of different kinds of chaotic data obtained from dynamical system has also been discussed in detail.展开更多
The state space, reconstruction is the major important quantitative index for describing non-linear chaotic time series. Based on the work of many scholars, such as: AT. H. Packard, F. Takens, M. Casdagli, J. F. Gibso...The state space, reconstruction is the major important quantitative index for describing non-linear chaotic time series. Based on the work of many scholars, such as: AT. H. Packard, F. Takens, M. Casdagli, J. F. Gibson, CHEN Yu-shu et al, the state space was reconstructed using the method of Legendre coordinate. Several different scaling regimes for lag time tau were identified. The influence for state space reconstruction of lag time tau was discussed. The result tells us that is a good practical method for state space reconstruction.展开更多
Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with...Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with high horticulture value need to be explored.Both problems largely hinder utilization of germplasm resources.Most studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic signals.Here,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral state.Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data.Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron.Subg.Therorhodion(cladeⅠ)formed the basal lineage.Subg.Tsutsusi and Azaleastrum formed cladeⅡand had sister relationships.CladeⅢincluded all scaly rhododendron species.Subg.Pentanthera(cladeⅣ)formed a sister group to Subg.Hymenanthes(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple color.This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data.It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships.Additionally,the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.展开更多
Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, ...Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.展开更多
文摘We present a simulation for the reconstruction of the rotational quantum state of linear molecules to retrieve the density matrix. An optimal approach in the sense of minimal error limit is proposed, in which a variable set of angular frequency is properly chosen and the least square inversion is then applied. This approach of reconstruction from time-dependent molecular-axis angular distribution is proved adaptable for various object states, which has a good numerical stability independent of the selected rotational space.
文摘We establish a reconstruction approach for the rotational quantum state of linear molecules possessing a magnetic manifold. Our approximate method contains an iteration with generalized matrix inverses, processing the tomographic integral of the time-dependent molecular-axis distribution in a polar angle. As shown in a simulated example for an alignment state, the density matrix is determined in a high fidelity. An analytic tomographic formula is also derived for the symmetric top rotation. The state coherent in the quantum space of both the angular momentum and its magnetic projection can be approximately retrieved from the observable time-resolved solid-angle distribution of the molecular axis.
文摘The state reconstruction problem is addressed for complex dynamical networks coupled with states and outputs respectively, in a noisy transmission channel. By using Lyapunov stability theory and H∞ performance, two schemes of state reconstruction are proposed for the complex dynamical networks with the nodes coupled by states and outputs respectively, and the estimation errors are convergent to zeros with H∞ performance index. A numerical simulation demonstrates the effectiveness of the proposed observers.
基金This work was supported by a grant of the Spanish Ministerio de Economía y Competitividad and FEDER CGL2013-40924-P,CGL2017-89898-R(AEI/FEDER,UE)a BiodivERsA:EC21C ERANet grant to DRV.RP was supported by an FPU predoctoral fellowship from the Spanish Ministerio de Educación.
文摘Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of traits.The development of ancestral state reconstruction(ASR)methods has provided the tools to reconstruct trait evolution,which are widely used in fields like evolutionary biology,macroecology and paleontology.As there are different elements involved in those analyses,with different levels of uncertainty(i.e.relating to branch length estimation,trait coding,statistical framework,taxon sampling or software),the various combinations of these elements likely have a strong impact on the reconstruction of the evolution of traits,potentially leading to opposite conclusions.To assess the impact of these different elements in ASR,we performed a set of analyses,including all possible combinations of such elements and using the evolution of migratory behavior in Sylvia warblers as a case study,which was coded as a continuous or as a discrete character.Our results show that taxon sampling,character coding,tree shape,statistical framework and software all significantly affect ASR,both individually and in combination.Not all reconstructed tree nodes show discrepancies,but in the critical ones most pairwise comparisons between analyses lead to conflicting and unexpectedly antagonistic results(zero migration vs fully migratory),thus challenging interpretations of trait evolution.We propose some possible solutions to partly inform decisions,involving the method selection and the incorporation of biological or fossil evidence regarding how traits evolve,but our results demand serious rethinking about how the research community currently uses ASR.
基金The project supported by the National Natural Science Foundation of China(19672043)
文摘Certain deterministic nonlinear systems may show chaotic behavior. We consider the motion of qualitative information and the practicalities of extracting a part from chaotic experimental data. Our approach based on a theorem of Takens draws on the ideas from the generalized theory of information known as singular system analysis. We illustrate this technique by numerical data from the chaotic region of the chaotic experimental data. The method of the singular-value decomposition is used to calculate the eigenvalues of embedding space matrix. The corresponding concrete algorithm to calculate eigenvectors and to obtain the basis of embedding vector space is proposed in this paper. The projection on the orthogonal basis generated by eigenvectors of timeseries data and concrete paradigm are also provided here. Meanwhile the state space reconstruction technology of different kinds of chaotic data obtained from dynamical system has also been discussed in detail.
基金the National Natural Science Foundation of China(19990510)
文摘The state space, reconstruction is the major important quantitative index for describing non-linear chaotic time series. Based on the work of many scholars, such as: AT. H. Packard, F. Takens, M. Casdagli, J. F. Gibson, CHEN Yu-shu et al, the state space was reconstructed using the method of Legendre coordinate. Several different scaling regimes for lag time tau were identified. The influence for state space reconstruction of lag time tau was discussed. The result tells us that is a good practical method for state space reconstruction.
基金supported by Ten Thousand Talent Program of Yunnan Province(Grant No.YNWR-QNBJ-2018-174)the Key Basic Research Program of Yunnan Province,China(Grant No.202101BC070003)+3 种基金National Natural Science Foundation of China(Grant No.31901237)Conservation Program for Plant Species with Extremely Small Populations in Yunnan Province(Grant No.2022SJ07X-03)Key Technologies Research for the Germplasmof Important Woody Flowers in Yunnan Province(Grant No.202302AE090018)Natural Science Foundation of Guizhou Province(Grant No.Qiankehejichu-ZK2021yiban 089&Qiankehejichu-ZK2023yiban 035)。
文摘Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with high horticulture value need to be explored.Both problems largely hinder utilization of germplasm resources.Most studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic signals.Here,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral state.Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data.Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron.Subg.Therorhodion(cladeⅠ)formed the basal lineage.Subg.Tsutsusi and Azaleastrum formed cladeⅡand had sister relationships.CladeⅢincluded all scaly rhododendron species.Subg.Pentanthera(cladeⅣ)formed a sister group to Subg.Hymenanthes(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple color.This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data.It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships.Additionally,the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.
基金support from the National Institute of Environmental Health Sciences (USA) training grant to the NCSU Bioinformatics Research Centersupported by National Institutes of Health (USA) grant no.GM070806
文摘Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.