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Hierarchical molecular interfaces and solvation electrostatics 层次分子界面与溶剂化静电
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629291
C. Bajaj, S. Chen, Guoliang Xu, Qin Zhang, Wenqi Zhao
Electrostatic interactions play a significant role in determining the binding affinity of molecules and drugs. While significant effort has been devoted to the accurate computation of biomolecular electrostatics based on an all-atomic solution of the Poisson-Boltzmann (PB) equation for smaller proteins and nucleic acids, relatively little has been done to optimize the efficiency of electrostatic energetics and force computations of macromolecules at varying resolutions (also called coarse-graining). We have developed an efficient and comprehensive framework for computing coarse-grained PB electrostatic potentials, polarization energetics and forces for smooth multi-resolution representations of almost all molecular structures, available in the PDB. Important aspects of our framework include the use of variational methods for generating C2-smooth and multi-resolution molecular surfaces (as dielectric interfaces), a parameterization and discretization of the PB equation using an algebraic spline boundary element method, and the rapid estimation of the electrostatic energetics and forces using a kernel independent fast multipole method. We present details of our implementation, as well as several performance results on a number of examples.
静电相互作用在决定分子和药物的结合亲和力方面起着重要作用。基于泊松-玻尔兹曼(PB)方程的小蛋白质和核酸的全原子解的生物分子静电的精确计算已经投入了大量的努力,而在不同分辨率(也称为粗粒化)下优化静电能量学和大分子力计算的效率的工作相对较少。我们已经开发了一个高效和全面的框架,用于计算粗粒度PB静电势,极化能量和力,用于PDB中几乎所有分子结构的光滑多分辨率表示。我们的框架的重要方面包括使用变分方法来生成c2光滑和多分辨率分子表面(作为介电界面),使用代数样条边界元方法对PB方程进行参数化和离散化,以及使用核无关快速多极方法快速估计静电能量和力。我们给出了实现的细节,以及一些示例的性能结果。
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引用次数: 1
Discrete physics using metrized chains 使用度量链的离散物理
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629273
A. DiCarlo, F. Milicchio, A. Paoluzzi, V. Shapiro
Over the last fifty years, there have been numerous efforts to develop comprehensive discrete formulations of geometry and physics from first principles: from Whitney's geometric integration theory [33] to Harrison's theory of chainlets [16], including Regge calculus in general relativity [26, 34], Tonti's work on the mathematical structure of physical theories [30] and their discrete formulation [31], plus multifarious researches into so-called mimetic discretization methods [28], discrete exterior calculus [11, 12], and discrete differential geometry [2, 10]. All these approaches strive to tell apart the different mathematical structures---topological, differentiable, metrical---underpinning a physical theory, in order to make the relationships between them more transparent. While each component is reasonably well understood, computationally effective connections between them are not yet well established, leading to difficulties in combining and progressively refining geometric models and physics-based simulations. This paper proposes such a connection by introducing the concept of metrized chains, meant to establish a discrete metric structure on top of a discrete measure-theoretic structure embodied in the underlying notion of measured (real-valued) chains. These, in turn, are defined on a cell complex, a finite approximation to a manifold which abstracts only its topological properties. The algebraic-topological approach to circuit design and network analysis first proposed by Branin [7] was later extensively applied by Tonti to the study of the mathematical structure of physical theories [30]. (Co-)chains subsequently entered the field of physical modeling [4, 18, 24, 25, 31, 37], and were related to commonly-used discretization methods such as finite elements, finite differences, and finite volumes [1, 8, 21, 22]. Our modus operandi is characterized by the pivotal role we accord to the construction of a physically based inner product between chains. This leads us to criticize the emphasis placed on the choice of an appropriate dual mesh: in our opinion, the "good" dual mesh is but a red herring, in general.
在过去的五十年里,有许多努力从第一原理发展几何和物理的综合离散公式:从Whitney的几何积分理论[33]到Harrison的链链理论[16],包括广义相对论中的Regge微积分[26,34],Tonti对物理理论的数学结构[30]及其离散公式的研究[31],以及对所谓的模拟离散化方法[28]、离散外微积分[11,12]、离散微分几何[2,10]的各种研究。所有这些方法都力求区分支撑物理理论的不同数学结构——拓扑结构、可微结构、格律结构,以便使它们之间的关系更加透明。虽然每个组件都被很好地理解,但它们之间的计算有效联系尚未很好地建立,这导致在组合和逐步完善几何模型和基于物理的模拟方面存在困难。本文通过引入度量链的概念提出了这样一种联系,即在隐含在度量链(实值链)概念中的离散测度论结构之上建立一个离散度量结构。这些,反过来,是定义在一个细胞复合体,一个有限的近似流形,抽象其拓扑性质。首先由Branin[7]提出的电路设计和网络分析的代数-拓扑方法后来被Tonti广泛应用于物理理论的数学结构研究[30]。(Co-)链随后进入物理建模领域[4,18,24,25,31,37],与常用的有限元、有限差分、有限体积等离散化方法有关[1,8,21,22]。我们的工作方式的特点是,我们同意在链之间建立一个基于物理的内部产品的关键作用。这导致我们批评强调选择合适的双网格:在我们看来,一般来说,“好的”双网格只是转移注意力。
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引用次数: 17
A framework for preservable geometry-centric artifacts 可保存的以几何为中心的工件的框架
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629265
W. Regli, Michael Grauer, Joseph B. Kopena
Digital preservation is the mitigation of the deleterious effects of technology obsolescence, media degradation, and fading human memory. For engineering, design, manufacturing, and physics-based simulation data this requires formats that are semantically accessible for 30-to-50 year lifespans. One of the fundamental challenges is the development of digital geometry-centric engineering representations that are self describing and assured to be interpretable over the long lifespans required by archival applications. This paper introduces the challenge of long-term preservation of digital geometric models. We describe a digital preservation case study for an engineering model which required, for just a single part, over 3.5 GB of data, including 39 file formats and over 750 distinct model and shape files. Based on lessons learned in this case study, we present a framework for enhancing the preservation of geometry-centric engineering knowledge. This framework is currently being used on a number of projects in engineering education.
数字保存是减轻技术过时、媒介退化和人类记忆衰退的有害影响。对于工程、设计、制造和基于物理的仿真数据,这需要在语义上可访问30至50年寿命的格式。其中一个基本的挑战是以数字几何为中心的工程表示的发展,这些表示是自我描述的,并且保证在档案应用程序所需的长寿命期间可以解释。本文介绍了数字几何模型长期保存所面临的挑战。我们描述了一个工程模型的数字保存案例研究,该模型只需要一个零件,超过3.5 GB的数据,包括39种文件格式和超过750种不同的模型和形状文件。基于本案例研究的经验教训,我们提出了一个增强以几何为中心的工程知识保存的框架。这个框架目前正在工程教育的一些项目中使用。
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引用次数: 5
Reliable sweeps 可靠的清洁工
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629306
Xinyu Zhang, Young J. Kim, Dinesh Manocha
We present a simple algorithm to generate a topology-preserving, error-bounded approximation of the outer boundary of the volume swept by a polyhedron along a parametric trajectory. Our approach uses a volumetric method that generates an adaptive volumetric grid, computes signed distance on the grid points, and extracts an isosurface from the distance field. In order to guarantee geometric and topological bounds, we present a novel sampling and front propagation algorithm for adaptive grid generation. We highlight the performance of our algorithm on many complex benchmarks that arise in geometric and solid modeling, motion planning and CNC milling applications. To the best of our knowledge, this is the first practical algorithm that can generate swept volume approximations with geometric and topological guarantees on complex polyhedral models swept along any parametric trajectory.
我们提出了一种简单的算法来生成一个拓扑保持的,误差有界的逼近由多面体沿参数轨迹扫过的体积的外边界。我们的方法使用体积法生成自适应体积网格,计算网格点上的符号距离,并从距离场提取等值面。为了保证几何边界和拓扑边界,提出了一种新的自适应网格生成的采样和前传播算法。我们强调了我们的算法在几何和实体建模,运动规划和数控铣削应用中出现的许多复杂基准上的性能。据我们所知,这是第一个能够在沿任何参数轨迹扫描的复杂多面体模型上生成具有几何和拓扑保证的扫描体积近似的实用算法。
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引用次数: 17
Accelerating geometric queries using the GPU 使用GPU加速几何查询
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629281
A. Krishnamurthy, Sara McMains, Kirk Haller
We present practical algorithms for accelerating geometric queries on models made of NURBS surfaces using programmable Graphics Processing Units (GPUs). We provide a generalized framework for using GPUs as co-processors in accelerating CAD operations. By attaching the data corresponding to surface-normals to a surface bounding-box structure, we can calculate view-dependent geometric features such as silhouette curves in real time. We make use of additional surface data linked to surface bounding-box hierarchies on the GPU to answer queries such as finding the closest point on a curved NURBS surface given any point in space and evaluating the clearance between two solid models constructed using multiple NURBS surfaces. We simultaneously output the parameter values corresponding to the solution of these queries along with the model space values. Though our algorithms make use of the programmable fragment processor, the accuracy is based on the model space precision, unlike earlier graphics algorithms that were based only on image space precision. In addition, we provide theoretical bounds for both the computed minimum distance values as well as the location of the closest point. Our algorithms are at least an order of magnitude faster than the commercial solid modeling kernel ACIS.
我们提出了实用的算法来加速几何查询模型上的NURBS表面使用可编程图形处理单元(gpu)。我们提供了一个使用gpu作为辅助处理器来加速CAD操作的通用框架。通过将表面法线对应的数据附加到表面边界盒结构上,我们可以实时计算出与视图相关的几何特征,如轮廓曲线。我们利用与GPU上的表面边界盒层次结构相关联的附加表面数据来回答查询,例如在给定空间中的任何点的弯曲NURBS表面上找到最近的点,以及评估使用多个NURBS表面构建的两个实体模型之间的间隙。我们同时输出与这些查询的解相对应的参数值以及模型空间值。虽然我们的算法使用了可编程片段处理器,但精度是基于模型空间精度的,而不像以前的图形算法只基于图像空间精度。此外,我们为计算的最小距离值和最近点的位置提供了理论界限。我们的算法至少比商业实体建模内核ACIS快一个数量级。
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引用次数: 8
Treedecomposition of geometric constraint graphs based on computing graph circuits 基于计算图电路的几何约束图的树分解
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629270
R. Joan-Arinyo, Marta I. Tarrés-Puertas, S. Vila-Marta
The graph-based geometric constraint solving technique works in two steps. First the geometric problem is translated into a graph whose vertices represent the set of geometric elements and whose edges are the constraints. Then the constraint problem is solved by decomposing the graph into a collection of subgraphs each representing a standard problem which is solved by a dedicated equational solver. In this work we report on an algorithm to decompose biconnected tree-decomposable graphs representing either under-or wellconstrained 2D geometric constraint problems. The algorithm recursively first computes a set of fundamental circuits in the graph then splits the graph into a set of subgraphs each sharing exactly three vertices with the fundamental circuit. Practical experiments show that the reported algorithm clearly outperforms the treedecomposition approach based on identifying subgraphs by applying specific decomposition rules.
基于图的几何约束求解技术分为两个步骤。首先,将几何问题转化为图,其顶点表示几何元素的集合,其边是约束条件。然后,通过将图分解为代表一个标准问题的子图集合来求解约束问题,每个子图由专用的方程求解器求解。在这项工作中,我们报告了一种分解表示欠约束或良好约束的二维几何约束问题的双连通树可分解图的算法。该算法首先递归地计算图中的一组基本电路,然后将图分成一组子图,每个子图与基本电路共享恰好三个顶点。实际实验表明,该算法明显优于基于特定分解规则识别子图的树分解方法。
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引用次数: 6
Configuration products in geometric modeling 配置产品的几何造型
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629286
S. Nelaturi, V. Shapiro
The six-dimensional space SE(3) is traditionally associated with the space of configurations of a rigid solid (a subset of Euclidean three-dimensional space E3). But a solid can be also considered to be a set of configurations, and therefore a subset of SE(3). This observation removes the artificial distinction between shapes and their configurations, and allows formulation and solution of a large class of problems in mechanical design and manufacturing. In particular, the configuration product of two subsets of configuration space is the set of all configurations obtained when one of the sets is transformed by all configurations of the other. The usual definitions of various sweeps, Minkowski sum, and other motion related operations are then realized as projections of the configuration product into E3. Similarly, the dual operation of configuration quotient subsumes the more common operations of unsweep and Minkowski difference. We identify the formal properties of these operations that are instrumental in formulating and solving both direct and inverse problems in computer aided design and manufacturing. Finally, we show that all required computations may be implemented using a fast parallel sampling method on a GPU.
六维空间SE(3)传统上与刚性实体(欧几里德三维空间E3的一个子集)的构型空间相关联。但一个实体也可以被认为是构型的集合,因此是SE(3)的子集。这种观察消除了形状和结构之间的人为区别,并允许在机械设计和制造中提出和解决一大类问题。特别地,构型空间的两个子集的构型积是其中一个子集被另一个子集的所有构型变换后得到的所有构型的集合。各种扫描、闵可夫斯基和和其他运动相关操作的通常定义随后被实现为配置积到E3的投影。同样,构商的对偶运算包含了更常见的反扫和闵可夫斯基差运算。我们确定了这些操作的形式属性,这些操作有助于制定和解决计算机辅助设计和制造中的直接和反问题。最后,我们证明了所有需要的计算都可以在GPU上使用快速并行采样方法来实现。
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引用次数: 13
Nonlinear systems solver in floating-point arithmetic using LP reduction 用LP约简的浮点算法求解非线性系统
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629271
Christoph Fünfzig, D. Michelucci, S. Foufou
This paper presents a new solver for systems of nonlinear equations. Such systems occur in Geometric Constraint Solving, e.g., when dimensioning parts in CAD-CAM, or when computing the topology of sets defined by nonlinear inequalities. The paper does not consider the problem of decomposing the system and assembling solutions of subsystems. It focuses on the numerical resolution of well-constrained systems. Instead of computing an exponential number of coefficients in the tensorial Bernstein basis, we resort to linear programming for computing range bounds of system equations or domain reductions of system variables. Linear programming is performed on a so called Bernstein polytope: though, it has an exponential number of vertices (each vertex corresponds to a Bernstein polynomial in the tensorial Bernstein basis), its number of hyperplanes is polynomial: O(n2) for a system in n unknowns and equations, and total degree at most two. An advantage of our solver is that it can be extended to non-algebraic equations. In this paper, we present the Bernstein and LP polytope construction, and how to cope with floating point inaccuracy so that a standard LP code can be used. The solver has been implemented with a primal-dual simplex LP code, and some implementation variants have been analyzed. Furthermore, we show geometric-constraint-solving applications, as well as numerical intersection and distance computation examples.
本文提出了一种求解非线性方程组的新方法。这种系统出现在几何约束求解中,例如,在CAD-CAM中标注零件尺寸时,或在计算由非线性不等式定义的集合的拓扑时。本文没有考虑系统的分解和子系统解的装配问题。它侧重于良好约束系统的数值分辨率。我们不是在张量Bernstein基中计算系数的指数数,而是采用线性规划来计算系统方程的范围边界或系统变量的域约简。线性规划是在所谓的Bernstein多面体上执行的:尽管它具有指数数量的顶点(每个顶点对应于张量Bernstein基中的Bernstein多项式),其超平面的数量是多项式:对于有n个未知数和方程的系统,其总度最多为2。我们的求解器的一个优点是它可以推广到非代数方程。在本文中,我们提出了Bernstein和LP多面体的构造,以及如何处理浮点不精确,使一个标准的LP代码可以使用。用原始对偶单纯形LP代码实现了该求解器,并分析了一些实现变体。此外,我们还展示了几何约束求解的应用,以及数值相交和距离计算的例子。
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引用次数: 19
Testing an axis of rotation for 3D workpiece draining 测试用于3D工件排水的旋转轴
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629283
Y. Yasui, Sara McMains
Given a triangular mesh defining the geometry of a 3D workpiece filled with water, we propose an algorithm to test whether, for an arbitrary given axis, the workpiece will be completely drained under gravity when rotated around the axis. Observing that all water traps contain a concave vertex, we solve our problem by constructing and analyzing a directed "draining graph" whose nodes correspond to concave vertices of the geometry and whose edges are set according to the transition of trapped water when we rotate the workpiece around the given axis. Our algorithm to check whether or not a given rotation axis drains the workpiece outputs a result in about a second for models with more than 100,000 triangles.
给定一个三角形网格来定义一个充满水的三维工件的几何形状,我们提出了一种算法来测试,对于任意给定的轴,工件在绕轴旋转时是否会在重力作用下完全排干。观察到所有的水陷阱都包含一个凹顶点,我们通过构造和分析一个有向的“排水图”来解决我们的问题,该图的节点对应于几何图形的凹顶点,并且当我们围绕给定轴旋转工件时,其边缘是根据捕获水的过渡设置的。我们的算法用于检查给定的旋转轴是否排出工件,对于具有超过100,000个三角形的模型,大约在一秒钟内输出结果。
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引用次数: 3
Tracing ridges on B-Spline surfaces 在b样条曲面上描脊
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629263
Suraj Musuvathy, E. Cohen, Joon-Kyung Seong, J. Damon
Ridges are characteristic curves of a surface that mark salient intrinsic features of its shape and are therefore valuable for shape matching, surface quality control, visualization and various other applications. Ridges are loci of points on a surface where either of the principal curvatures attain a critical value in its respective principal direction. These curves have complex behavior near umbilics on a surface, and may also pass through certain turning points causing added complexity for ridge computation. We present a new algorithm for numerically tracing ridges on B-Spline surfaces that also accurately captures ridge behavior at umbilics and ridge turning points. The algorithm traverses ridge segments by detecting ridge points while advancing and sliding in principal directions on a surface in a novel manner, thereby computing connected curves of ridge points. The output of the algorithm is a set of curve segments, some or all of which, may be selected for other applications such as those mentioned above. The results of our technique are validated by comparison with results from previous research and with a brute-force domain sampling technique.
脊是表面的特征曲线,它标志着其形状的显著内在特征,因此对形状匹配,表面质量控制,可视化和各种其他应用具有价值。脊是曲面上任一主曲率在其各自主方向上达到临界值的点的轨迹。这些曲线在地面的脐带附近具有复杂的行为,并且还可能通过某些拐点,从而增加了脊计算的复杂性。我们提出了一种新的b样条曲面上的数值跟踪脊的算法,该算法还可以准确地捕获脐带和脊转折点的脊行为。该算法以一种新颖的方式,通过检测脊点,同时在曲面上进行主方向的移动和滑动,从而遍历脊段,从而计算脊点的连接曲线。该算法的输出是一组曲线段,其中一些或全部可以选择用于其他应用,例如上面提到的应用。通过与先前研究结果的比较以及与暴力域采样技术的比较,验证了我们技术的结果。
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引用次数: 5
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Symposium on Solid and Physical Modeling
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