基于拓扑子集的势场原子类型的派定

对于除了标准氨基酸、核酸残基以外的一般分子,派定分子中原子的原子类型,确定原子类型在不同分子势场之间的转换,这些工作一般是由人工来完成。本文从分子拓扑学的角度解析了分子势场的原子类型(atom type)定义,以基于分子拓扑子集取代原子类型定义的分子片断为途径,实现势场原子类型的计算机自动派定。该方法易于编程,并能满足用户调整原子类型的意愿。     

Enumeration of Kekulé structures in polyradical polyhexes

A set of recurrent reduction rules for polyradical polyhex skeletons is presented. This algorithm enables for us not only to enumerate and realize Kekulé structures in polyradical skeletons, but also to investigate the topological and/or graph-theoretical property of the structures.     

Topological spines: a structure-preserving visual representation of scalar fields

We present topological spines--a new visual representation that preserves the topological and geometric structure of a scalar field. This representation encodes the spatial relationships of the extrema of a scalar field together with the local volume and nesting structure of the surrounding contours. Unlike other topological representations, such as contour trees, our approach preserves the local geometric structure of the scalar field, including structural cycles that are useful for exposing symmetries in the data. To obtain this representation, we describe a novel mechanism based on the extraction of extremum graphs--sparse subsets of the Morse-Smale complex that retain the important structural information without the clutter and occlusion problems that arise from visualizing the entire complex directly. Extremum graphs form a natural multiresolution structure that allows the user to suppress noise and enhance topological features via the specification of a persistence range. Applications of our approach include the visualization of 3D scalar fields without occlusion artifacts, and the exploratory analysis of high-dimensional functions.     

NESTED ALGORITHMIC SKELETONS FROM HIGHER ORDER FUNCTIONS

Algorithmic skeletons provide a promising basis for the automatic utilisation of parallelism at sites of higher order function use through static program analysis. However, decisions about whether or not to realise particular higher order function instances as skeletons must be based on information about processing resources available at runtime

In principle, nested higher order functions may be realised as nested skeletons. However, where higher order function arguments result from partially applied functions, free-variable bindings must be identified and communicated through the corresponding skeleton hierarchy to where those arguments are actually applied

Here, a skeleton based parallelising compiler for Standard ML is presented. Hybrid skeletons, which can change from parallel to serial evaluation at runtime, are considered and mechanisms for their nesting are discussed. The main compilation stages are illustrated for simple examples. A nested higher order function based algorithm for multiplying matrices of arbitrary length integers is presented along with performance figures for compiled code running on a Fujitsu AP3000.     

Materials Studio软件涉及力场中氢键的研究

利用Materials Studio(MS)材料科学软件,分别采用pcff、COMPASS及cvff力场．计算两个乙醇分子间的氢键作用,考察了氢原子和受体氧原子间距离、成键角度等因素对各种非键作用能的影响。研究结果表明:(1)当将氢链作用看成是范德华作用和静电作用的综合结果时,对氢键的反映cvff最差,COMPASS最好;(2)只要采用合适的范德华作用势函数、力常数以及指定恰当的原子部分电荷,是可以用一般的非键作用来反映氢键的。本文为MS用户初步解释了MS中的力场是如何处理氢键的重要疑问。     

一个标识子系统的设计与实现

特征造型的关键是合理地确定新旧模型拓扑元素之间的对应关系，文中提出一个基于特征的标识子系统，使得产品模型中每个拓扑元素都对应一个唯一的标识，标识匹配算法可以建立新旧模型拓扑元素之间的对应关系，标识子系统是作者开发的特征造型系统GDS的重要线成部分，为特征编辑、语义操作，二三维约束统一求解等奠定了基础。     

Topology-preserving smoothing of vector fields

Proposes a technique for topology-preserving smoothing of sampled vector fields. The vector field data is first converted into a scalar representation in which time surfaces implicitly exist as level sets. We then locally analyze the dynamic behavior of the level sets by placing geometric primitives in the scalar field and by subsequently distorting these primitives with respect to local variations in this field. From the distorted primitives, we calculate the curvature normal and we use the normal magnitude and its direction to separate distinct flow features. Geometrical and topological considerations are then combined to successively smooth dense flow fields, at the same time retaining their topological structure     

Interactive comparison of scalar fields based on largest contours with applications to flow visualization

Understanding fluid flow data, especially vortices, is still a challenging task. Sophisticated visualization tools help to gain insight. In this paper, we present a novel approach for the interactive comparison of scalar fields using isosurfaces, and its application to fluid flow datasets. Features in two scalar fields are defined by largest contour segmentation after topological simplification. These features are matched using a volumetric similarity measure based on spatial overlap of individual features. The relationships defined by this similarity measure are ranked and presented in a thumbnail gallery of feature pairs and a graph representation showing all relationships between individual contours. Additionally, linked views of the contour trees are provided to ease navigation. The main render view shows the selected features overlapping each other. Thus, by displaying individual features and their relationships in a structured fashion, we enable exploratory visualization of correlations between similar structures in two scalar fields. We demonstrate the utility of our approach by applying it to a number of complex fluid flow datasets, where the emphasis is put on the comparison of vortex related scalar quantities.     

Image registration using Markov random coefficient and geometric transformation fields

Image registration is central to different applications such as medical analysis, biomedical systems, and image guidance. In this paper we propose a new algorithm for multimodal image registration. A Bayesian formulation is presented in which a likelihood term is defined using an observation model based on coefficient and geometric fields. These coefficients, which represent the local intensity polynomial transformations, as the local geometric transformations, are modeled as prior information by means of Markov random fields. This probabilistic approach allows one to find optimal estimators by minimizing an energy function in terms of both fields, making the registration between the images possible.     

Topological maps and robust hierarchical Euclidean skeletons in cubical complexes

Skeletons are notoriously sensitive to contour noise, and an effective filtering scheme is needed in any practical situation, where skeletons are involved. In this article, we introduce a new discrete framework that allows us to define and compute families of filtered Euclidean skeletons, in 2D as well as in 3D or higher dimensions. We prove several properties of our skeletonization scheme, in particular the preservation of topological characteristics and the stability with respect to parameter changes.     

基于骨架的隐曲面造型技术

为实现光滑物体的参数化特征造型，对巳有的基于骨架的隐曲面造型技术做了两项改进：（1）提出一个不同于传统的欧几里得距离定义的点到一般凸集骨架距离定义，使得基于点到骨架距离定义的一般凸集骨架所张成的曲面保留了点骨架所张成曲面-球面的所有特性，特别是曲面的高度光滑性和曲面的骨架表示的高度抽象性；（2）提出一种骨架生成场的融合方法，即累乘各个骨架生成场，与传统的融合方法相比，这种融合方法具有更好的融合特性。     

引入欧椋鸟群飞行机制的改进粒子群算法

传统粒子群算法存在早熟、精度低等不足,许多改进算法尽管性能略有提高,但依然存在原有弊端。生物学家对欧椋鸟群的最新研究发现:鸟群飞行机制中个体间存在拓扑相互作用,与距离远近无关。受这一研究成果启发,提出一种引入欧椋鸟飞行机制的改进粒子群算法。该算法在进化策略上引入拓扑作用和猎食动物的惊扰机制,在参数选择上提出粒子群动能的概念,在线性递减权重框架下通过粒子动能自适应更新惯性权重,拓扑作用集合采用最近邻粒子构成,将拓扑因子与惯性权重相联系,达到进化状态的平衡和自适应性。仿真实验表明,改进算法在精度、成功率和效率上具有一定的优势,尤其是对多模态优化问题。     

Dual stream function visualization of flows fields dependent on two variables

The construction of streamlines is one of the most common methods for visualising fluid motion. Streamlines can be computed from the intersection of two nonparallel stream surfaces, which are iso-surfaces of dual stream functions. Stream surfaces are also useful to isolate part of the flow domain for detailed study. This paper introduces a technique for calculating dual stream functions for momentum fields that are defined analytically and depend on only two variables. For axi-symmetric flows, one of the dual stream functions is the well-known Stokes stream function. The analysis reduces the problem from the solution of partial differential equations to the solution of two ordinary differential equations. Example applications include the Moffat [17] vortex bubble, for which new solutions are presented.     

Designing 2D Vector Fields of Arbitrary Topology

We introduce a scheme of control polygons to design topological skeletons for vector fields of arbitrary topology. Based on this we construct piecewise linear vector fields of exactly the topology specified by the control polygons. This way a controlled construction of vector fields of any topology is possible. Finally we apply this method for topology‐preserving compression of vector fields consisting of a simple topology.     

Distance functions and skeletal representations of rigid and non-rigid planar shapes

Shape skeletons are fundamental concepts for describing the shape of geometric objects, and have found a variety of applications in a number of areas where geometry plays an important role. Two types of skeletons commonly used in geometric computations are the straight skeleton of a (linear) polygon, and the medial axis of a bounded set of points in the k-dimensional Euclidean space. However, exact computation of these skeletons of even fairly simple planar shapes remains an open problem.In this paper we propose a novel approach to construct exact or approximate (continuous) distance functions and the associated skeletal representations (a skeleton and the corresponding radius function) for solid 2D semi-analytic sets that can be either rigid or undergoing topological deformations. Our approach relies on computing constructive representations of shapes with R-functions that operate on real-valued halfspaces as logic operations. We use our approximate distance functions to define a new type of skeleton, i.e, the C-skeleton, which is piecewise linear for polygonal domains, generalizes naturally to planar and spatial domains with curved boundaries, and has attractive properties. We also show that the exact distance functions allow us to compute the medial axis of any closed, bounded and regular planar domain. Importantly, our approach can generate the medial axis, the straight skeleton, and the C-skeleton of possibly deformable shapes within the same formulation, extends naturally to 3D, and can be used in a variety of applications such as skeleton-based shape editing and adaptive motion planning.     

Skeletal categories

We examine in this paper skeletons of deformed image categories and their connection with structures and projections. First we state under which conditions a subcategory Σ of the deformed image category ^Δ is a skeleton. Second, we consider the particular case when all deformations reduce themselves to similarities and compare Σ to the category of structures. Third, we establish a link between skeletons and projections. Indications are given about the topological explanation of the properties which skeletons and projections possess in common as well as about the connection existing between our formalism and current applications.     

Mining the Chemical Abstracts database with pharmacophore-based queries

A method is described to convert 3D patterns of pharmacophoric groups into 2D queries for molecular substructure searches of the Chemical Abstracts database with SciFinder Scholar. The results of such searches and the options for refinement of the hit lists are presented using a rigid tetrahydroisoquinoline-carbazole (IQC) hybrid molecule fitted onto previously developed pharmacophores for subtype-selective alpha1-adrenergic receptor antagonists as an example. The compounds retrieved were further analysed by limiting their physical properties to 'drug-like' ranges and by enumerating the ring skeletons they contain. Selected ring skeletons were evaluated by fitting them on to the original pharmacophores. Several structurally novel rigid ring skeletons were found with this new database mining technique which are potentially useful as leads in the design of alpha1B selective adrenergic receptor antagonists.     

Variational Curve Skeletons Using Gradient Vector Flow

Representing a 3D shape by a set of 1D curves that are locally symmetric with respect to its boundary (i.e., curve skeletons) is of importance in several machine intelligence tasks. This paper presents a fast, automatic, and robust variational framework for computing continuous, subvoxel accurate curve skeletons from volumetric objects. A reference point inside the object is considered a point source that transmits two wave fronts of different energies. The first front (beta-front) converts the object into a graph, from which the object salient topological nodes are determined. Curve skeletons are tracked from these nodes along the cost field constructed by the second front (alpha-front) until the point source is reached. The accuracy and robustness of the proposed work are validated against competing techniques as well as a database of 3D objects. Unlike other state-of-the-art techniques, the proposed framework is highly robust because it avoids locating and classifying skeletal junction nodes, employs a new energy that does not form medial surfaces, and finally extracts curve skeletons that correspond to the most prominent parts of the shape and hence are less sensitive to noise.     

Applicability of commonly used atom-atom type potential energy functions in structural analysis of nucleic acids. The role of electrostatic interactions

Applicability of five popular force fields (AMBER, CFF91, CVFF CHARMM and GROMOS) to the structural analysis of nucleic acids without explicit solvent has been examined. Structures of nine deoxyoligonucleotides in the A- and B-forms were optimized by energy minimization and compared with well-refined crystallographic data. Several models for electrostatic interactions were tested including constant and distance dependent dielectric functions in combination with varied effective charges of the phosphate groups. Similarity tests of the theoretical and experimental structures were based on a distance analysis in a conformational parameter space of the DNA molecules and on a proposed scoring scheme.