快速构造植物几何结构的子结构算法

顺序地模拟符合植物学生物特征的复杂树结构会占用很多计算机资源。为减少对计算机资源的占用，提出了一种从最简单的子结构起，通过子结构的引用来形成复杂结构的方法。由于在该方法中重复出现的结构只被计算一次，因此不仅可以提高复杂结构的计算速度，而且可以降低几何信息的存储量。该几何信息不仅包括所模拟植物在各个生长周期的结构，而且包括了每个子结构的具体形态。尽管这是一种自上而下的算法，但由于子结构方法能够实现弯曲枝条的模拟，并能产生重复生长的结构和花序结构，因此具有通用性。     

Characteristic substructures in sets of organic compounds with similar infrared spectra

A method based on the determination of maximum common substructures is applied for the generation of substructures which are characteristic for a given set of molecular structures. The molecular structures are from hitlists obtained by spectral library searches; the hitlists contain those reference compounds, which have infrared spectra most similar to that from the query compound. The influences of various parameters of this method are investigated with the aim to improve the relevance of the obtained substructures for the structure of the query compound.     

An improved method of substructure analysis

Substructure method is an established way of overcoming the difficulty of large dimensionality in analysing structures. An improved substructure analysis method suitable for structures like multi-storied buildings and towers is presented in this paper. The method is based on peculiar geometry of these structures which could be used for numbering the boundary joints for a substructure either in the beginning or towards the end. Extra advantage could also be taken of the substructures identical in terms of geometry and loading both or in terms of geometry alone. Special static condensation and substitutions routines are developed. The method is shown to be more efficient than any of the existing substructure analysis methods.     

An improved secondary structure computation method and its application to intervening sequence in the human alpha-like globin mRNA precursors

Current secondary structure prediction computations have a serious drawback. The calculated thermodynamically most stable structure often differs from that observed in solution or in crystal form. In this paper we suggest a way to partially over-come some of these limitations by simulating the RNA folding process and calculating the frequencies of occurrence of the various substructures obtained. The frequently recurring substructures are then selected to construct the secondary structure of the whole RNA. 142 tRNA molecules and an E. coli 16S rRNA molecule have been examined by this method. The percentage of successful prediction of the correct helices are significantly higher than those calculated previously. The secondary structures of intervening sequences (IVSs) excised from human alpha-like globin pre-mRNAs are also computed. Thus, in this method the secondary structures obtained are composed of the statistically more significant substructures. This has also been demonstrated by using randomly shuffled sequences. The secondary structures of each of the randomized sequences are computed and their mean and standard deviations are used in evaluating the significance of the substructures obtained in the folding of the biological sequence. Some potentially appealing structural features aligning adjacent exons for ligation have been found.     

ASES／MS结构解析系统的分子结构产生程序

本文介绍了ASES/MS结构解析系统的分子结构产生程序。该程序自动从未知物质谱的亚结构鉴定结果中选取合适的亚结构来组建候选分子结构,并在结构组建过程中自动处理参与组建分子结构的亚结构之间所有可能的结构重叠情况。结构组建过程采用了人工智能理论中的穷举宽度优先搜索算法,并配合以分子量的约束。程序即满足了结构组建的完全性和非冗余性,又具有较高的运行效率。     

Optimum structural design with parallel finite element analysis

Structural analysis is an important part of the optimum structural design process. Therefore, extra effort should be devoted to make this part as efficient as possible. Since finite element analysis is the most powerful and widely used tool in the structural analysis field, in this paper a new method for structural optimization by parallel finite element method is presented. This method divides the original structure into several substructures and assigns each substructure to one processor. Each processor handles its finite element calculation independently with limited communication between processors. Some numerical examples on the Cray X-MP multiprocessor system with their obtained speedups are presented.     

Analytical study of a stochastic plant growth model: Application to the GreenLab model

A stochastic functional–structural model simulating plant development and growth is presented. The number of organs (internodes, leaves and fruits) produced by the model is not only a key intermediate variable for biomass production computation, but also an indicator of model complexity. To obtain their mean and variance through simulation is time-consuming and the results are approximate. In this paper, based on the idea of substructure decomposition, the theoretical mean and variance of the number of organs in a plant structure from the model are computed recurrently by applying a compound law of generating functions. This analytical method provides fast and precise results, which facilitates model analysis as well as model calibration and validation with real plants. Furthermore, the mean and variance of the biomass production from the stochastic plant model are of special interest linked to the prediction of yield. In this paper, through differential statistics, their approximate results are computed in an analytical way for any plant age. A case study on sample trees from this functional–structural model shows the theoretical moments of the number of organs and the biomass production, as well as the computation efficiency of the analytical method compared to a Monte-Carlo simulation method. The advantages and the drawbacks of this stochastic model for agricultural applications are discussed.     

Crashworthiness optimization of helicopter subfloor based on decomposition and global approximation

This work deals with the development of an optimization procedure under crashworthiness requirements applied to a typical helicopter subfloor. The difficulties due to the nonlinear design space and structural behaviour are overcome by developing an optimization procedure based on decomposition, where the structure to be optimized is converted into a set of smaller and linked substructures. To evaluate the response of each substructure, global approximation strategies, based on neural networks, are used. Size variables (dimensions, thickness) and geometrical variables (element number and position) are considered in order to maximize the global crashworthiness performance. The energy absorbed per unit mass by the subfloor is chosen as objective function and acceleration constraints are considered. Genetic algorithms are used to find the optimal configuration. The optimization allowed an increase in the crush force efficiency of 12% and a decrease in the subfloor mass of 4%. A significant CPU time saving was also obtained.     

The application of component mode synthesis for the dynamic analysis of complex structures using ADINA

This paper describes how a complex structure is divided into various kinds of substructures which are calculated independently using the ADINA program and, following this, the dynamic characteristics of the entire structure are recombined by the bi-consistent dynamic substructure method which is a free-interface method improved by the authors. Because both the displacement consistent of substructure interfaces and the interface force equilibrium are satisfied by the present method, all interface degrees of freedom in the synthesis equations can be eliminated. Several examples are presented to illustrate the effectiveness of the proposed method.     

Studies of frequently recurring substructures in human alpha-like globin mRNA precursors

In general, the results obtained from secondary structure prediction algorithms are often inconsistent with those obtained experimentally. The reason for this disagreement is that the experimentally determined structures have higher free energies (as judged by the currently used "energy rules") than the predicted ones. To overcome this limitation we have developed a new approach which incorporates the frequencies of occurrence of substructures in the growing mRNA chain. This has been accomplished by simulating the folding process of pre-mRNAs. Using this approach we have significantly improved current helical structural prediction for 142 analyzed tRNAs and 16 S rRNA. We have next applied this method to the human alpha-like globins. Comparison of the structures obtained by running the currently used algorithms with those computed by the new method indicates that the final most stable secondary structure contains some infrequently occurring substructures. In addition, some of the frequently recurring substructures are not included in the final structure. Comparison of the simulated folding processes of the human alpha-like globin pre-mRNAs reveals some conserved helices and hairpin loop structures in those frequently recurring substructures. Among these several compensating base changes (transitions and transversions) have been identified.     

Variational-Based Reduced-Order Model in Dynamic Substructuring of Coupled Structures Through a Dissipative Physical Interface: Recent Advances

This paper deals with a variational-based reduced-order model in dynamic substructuring of two coupled structures through a physical dissipative flexible interface. We consider the linear elastodynamic of a dissipative structure composed of two main dissipative substructures perfectly connected through interfaces by a linking substructure. The linking substructure is flexible and is modeled in the context of the general linear viscoelasticity theory, yielding damping and stiffness operators depending on the frequency, while the two main dissipative substructures are modeled in the context of linear elasticity with an additional classical viscous damping modeling which is assumed to be independent of the frequency. We present recent advances adapted to such a situation, which is positioned with respect to an appropriate review that we carry out on the different methods used in dynamic substructuring. It consists in constructing a reduced-order model using the free-interface elastic modes of the two main substructures and, for the linking substructure, an appropriate frequency-independent elastostatic lifting operator and the frequency-dependent fixed-interface vector basis.     

Compliant assembly variation analysis of aeronautical panels using unified substructures with consideration of identical parts

The assembly process of aeronautical panel usually involves numerous parts and subprocesses. Thus a large number of Finite Element Analysis (FEA) runs are required to construct its compliant Deviation Propagation Model (DPM), when using the traditional compliant assembly variation analysis methods such as the Method of Influence Coefficients and the Linear Contact method. In this paper, an efficient DPM construction method based on substructures is proposed to reduce the modeling complexity. Finite element models of compliant parts are condensed into substructures which have relatively fewer Degrees of Freedom (DOFs). And for the identical parts commonly used in the aeronautical panels, once the substructure of one part is generated, the substructures of the others can be obtained by transformation of the generated one. By properly selecting the retained DOFs, the same substructures are applicative throughout the overall modeling process. Based on these unified substructures, the DPM of aeronautical panel assembly process is constructed, without executing extra FEA runs. A case study on a panel subassembly of the side fuselage is used to illustrate the proposed method. The results show that, this method reduces the model size as well as the model construction work, while maintaining the same accuracy as complete finite element analysis conducted in a commercial software package.     

BLISS/S: a new method for two-level structural optimization

The paper describes a two-level method for structural optimization for a minimum weight under the local strength and displacement constraints. The method divides the optimization task into separate optimizations of the individual substructures (in the extreme, the individual components) coordinated by the assembled structure optimization. The substructure optimizations use local cross-sections as design variables and satisfy the highly nonlinear local constraints of strength and buckling. The design variables in the assembled structure optimization govern the structure overall shape and handle the displacement constraints. The assembled structure objective function is the objective in each of the above optimizations. The substructure optimizations are linked to the assembled structure optimization by the sensitivity derivatives. The method was derived from a previously reported two-level optimization method for engineering systems, e.g. aerospace vehicles, that comprise interacting modules to be optimized independently, coordination provided by a system-level optimization. This scheme was adapted to structural optimization by treating each substructure as a module in a system, and using the standard finite element analysis as the system analysis. A numerical example, a hub structure framework, is provided to show the new method agreement with a standard, no-decomposition optimization. The new method advantage lies primarily in the autonomy of the individual substructure optimization that enables concurrency of execution to compress the overall task elapsed time. The advantage increases with the magnitude of that task. Received December 5, 1999?Revised mansucript received April 26, 2000     

Improved group-theoretical method for eigenvalue problems of special symmetric structures,using graph theory

Group-theoretical methods for decomposition of eigenvalue problems of skeletal structures with symmetry employ the symmetry group of the structures and block-diagonalize their matrices. In some special cases, such decompositions can further be continued. This particularly happens when submatrices resulted from the decomposition process, correspond to substructures with new symmetrical properties which are not among the properties of the original structure. Thus, a group-theoretical method is not able to recognize such additional symmetry from the original problem. In this paper, an algorithm is presented based upon a combination of group-theoretical ideas and graph-methods. This algorithm identifies the cases where the structure has the potential of being further decomposed, and also finds the symmetry group, and subsequently the transformation which can further decompose the system. It is also possible to find out when the block-diagonalization is complete and no further decomposition is possible. This is particularly useful for large eigenvalue problems such as calculation of the buckling load or natural frequencies of vibrating systems with special symmetries.     

基于多属性的空间连续模糊聚类算法的血管分割

血管系统的3维显示对于图像导航神经外科和手术计划非常重要。提出了一种基于多属性的空间连续模糊聚类算法的血管分割算法来提取时飞磁共振血管造影（TOF MRA)图像中的血管,该聚类算法同时利用了图像的灰度信息和几何信息来提取血管,而目前已有算法仅采用灰度信息。在该算法中又提出了一个融合了灰度和几何形状的不相似性度量准则, 由于几何形状的采用,使得该算法可以区分具有相似灰度但位于不同几何形状组织里的像素。为了验证该算法,分别对2维和3维图像进行了分割,实验结果表明,该算法能够获得更好的分割结果。     

荠菜根系的计算机模拟

针对荠菜根系的形态特征和生长特点,提出一种基于几何模型的荠菜根系三维建模方法：根据荠菜根系的拓扑几何结构,应用根系几何模型SimRoot,基于Visual C++平台并采用OpenGL图形库,建立能较真实再现荠菜根系动态生长过程的可视化模拟系统。模拟结果表明该方法是可行有效的。     

PlantGL: A Python-based geometric library for 3D plant modelling at different scales

In this paper, we present PlantGL, an open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants. This C++ geometric library is embedded in the Python language which makes it a powerful user-interactive platform for plant modeling in various biological application domains.PlantGL makes it possible to build and manipulate geometric models of plants or plant parts, ranging from tissues and organs to plant populations. Based on a scene graph augmented with primitives dedicated to plant representation, several methods are provided to create plant architectures from either field measurements or procedural algorithms. Because they are particularly useful in plant design and analysis, special attention has been paid to the definition and use of branching system envelopes. Several examples from different modelling applications illustrate how PlantGL can be used to construct, analyse or manipulate geometric models at different scales ranging from tissues to plant communities.     

Analysis of stub-girders using substructuring

This paper deals with the application of the method of substructures to calculate deflections in stub-girders. A stub-girder is a new type of composite beam recently introduced in the United States. It consists of a steel beam and a reinforced concrete slab separated by a series of short steel rolled sections called stubs. The openings between the adjacent stubs are used as service ducts.Since most of the panels of a stub-girder are identical in shape and size, the method of substructures, which requires the physical partitioning of the structure into smaller units, is particularly suitable for its analysis. For the analysis presented herein a substructure, i.e. a smaller unit of the stub-girder, was discretized into an assemblage of plane stress rectangular finite elements. The two dimensional analysis was chosen because a preliminary investigation indicated that the matrix storage requirements for a 3-D analysis were so large that the amount of storage and the cost of the analysis would be prohibitive for most practical cases.The method of analysis is illustrated by application to three stub-girders. The computed results were compared with those determined experimentally. Two different idealizations were used to replace the flanges. The computed deflection values for one of the idealizations showed acceptable agreement with the experimental results. The computer program developed for this investigation can also be used to calculate the deflection in a beam with a series of rectangular openings.