The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Padmini Rangamani - One of the best experts on this subject based on the ideXlab platform.
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an open source Mesh Generation platform for biophysical modeling using realistic cellular geometries
Biophysical Journal, 2020Co-Authors: Justin G Laughlin, John B Moody, Rommie E Amaro, Andrew J Mccammon, Michael Holst, Padmini RangamaniAbstract:Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric Mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this work, we outline the steps for a naive user to approach the Geometry-preserving Adaptive MeshER software version 2, a Mesh Generation code written in C++ designed to convert structural data sets to realistic geometric Meshes while preserving the underlying shapes. We present two example cases: 1) Mesh Generation at the subcellular scale as informed by electron tomography and 2) Meshing a protein with a structure from x-ray crystallography. We further demonstrate that the Meshes generated by the Geometry-preserving Adaptive MeshER software are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric Meshes from structural biology data.
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an open source Mesh Generation platform for biophysical modeling using realistic cellular geometries
bioRxiv, 2019Co-Authors: Justin G Laughlin, John B Moody, Rommie E Amaro, Andrew J Mccammon, Michael Holst, Padmini RangamaniAbstract:ABSTRACT Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric Mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a naive user to approach GAMer 2, a Mesh Generation code written in C++ designed to convert structural datasets to realistic geometric Meshes, while preserving the underlying shapes. We present two example cases, 1) Mesh Generation at the subcellular scale as informed by electron tomography, and 2) Meshing a protein with structure from x-ray crystallography. We further demonstrate that the Meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric Meshes from structural biology data. SIGNIFICANCE As biophysical structure determination methods improve, the rate of new structural data is increasing. New methods that allow the interpretation, analysis, and reuse of such structural information will thus take on commensurate importance. In particular, geometric Meshes, such as those commonly used in graphics and mathematics, can enable a myriad of mathematical analysis. In this work, we describe GAMer 2, a Mesh Generation library designed for biological datasets. Using GAMer 2 and associated tools PyGAMer and BlendGAMer, biologists can robustly generate computer and algorithm friendly geometric Mesh representations informed by structural biology data. We expect that GAMer 2 will be a valuable tool to bring realistic geometries to biophysical models.
Jianjun Chen - One of the best experts on this subject based on the ideXlab platform.
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parallel and automatic isotropic tetrahedral Mesh Generation of misaligned assemblies
IEEE International Conference on High Performance Computing Data and Analytics, 2020Co-Authors: Peng Zheng, Yang Yang, Zhiwei Liu, Junji Wang, Juelin Leng, Tiantian Liu, Zhaoxu Zhu, Jianjun ChenAbstract:Mesh Generation is a challenge for high-performance numerical simulation, one reason is the complex geometry representing solution domain makes pre-processing difficult, especially for those assembly model containing hundreds and thousands of components involving misaligned interfaces between neighboring parts, and no state-of-art Meshing tools could provide automatic functions for processing such complex model, another reason is hundreds of millions or even billions Meshes should be generated quickly, which also exceeds the capabilities of available tools. In this paper, a novel parallel and automatic Mesh Generation method is proposed. Firstly, a surface imprinting algorithm based on the hybrid representation of discrete and continuous surfaces is proposed to process misaligned assembly model automatically. Then, the repaired assembly model is used as an input for a carefully designed Mesh Generation pipeline which connects the procedures of Mesh sizing control, and three-level parallel tetrahedral Mesh Generation in order. This proposed method could produce hundreds of millions consistent Mesh qualified for high-performance numerical simulation based on thousands of geometry components. Numerical experiments on a giant dam model and an integrated circuit board model demonstrates the effectiveness of this method.
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a boundary element based automatic domain partitioning approach for semi structured quad Mesh Generation
Engineering Analysis With Boundary Elements, 2020Co-Authors: Zhoufang Xiao, Jianjun ChenAbstract:Abstract In this paper, a boundary element-based approach is proposed for partitioning a planar domain automatically into a set of 4-sided regions, which is suitable for semi-structured quad Mesh Generation. The basic idea is to generate a smooth cross-field via solving PDEs with the boundary element method and then partition the input domain by extracting singular structures of the cross-field. Firstly, a cross is configured at each boundary vertex of the input domain. Then, two Laplacian equations are selected as the governing equation to smoothly propagate the crosses defined on the boundary into the interior of the domain. To obtain an accurate cross-field, the boundary element method is used to solve the governing equations. Then the singular vertices are identified by analyzing the structure of the cross-field, and the streamlines emanating from these points are traced and simplified as segmentation curves to partition the domain. Finally, to demonstrate the efficiency and effectiveness of the proposed approach, some quad Mesh Generation examples and comparison with previous approaches are presented.
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improvements in the reliability and element quality of parallel tetrahedral Mesh Generation
International Journal for Numerical Methods in Engineering, 2012Co-Authors: Jianjun Chen, Yao Zheng, Dawei Zhao, Zhengge Huang, Desheng WangAbstract:SUMMARY The paper presents a parallel tetrahedral Mesh Generation approach based on recursive bidivisions using triangular surfaces. Research was conducted for addressing issues concerning Mesh Generation reliability and element quality. A novel procedure employing local modification techniques is proposed for repairing the intersecting interdomain Mesh instead of directly repeating the bidivision procedure, which improves the robustness of the complete Meshing procedure significantly. In addition, a new parallel quality improvement scheme is suggested for optimizing the distributed volume Meshes. The scheme is free of any communication cost and highly efficient. Finally, Mesh experiments of hundreds of millions of elements are performed to demonstrate the reliability, effectiveness and efficiency of the proposed method and its potential applications to large-scale simulations of complex aerodynamics models. Copyright © 2012 John Wiley & Sons, Ltd.
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scalable parallel quadrilateral Mesh Generation coupled with Mesh partitioning
Parallel and Distributed Computing: Applications and Technologies, 2005Co-Authors: Jianjun Chen, Yao Zheng, Xia NingAbstract:In this paper, we present our efforts to parallelize an unstructured quadrilateral Mesh generator. Its serial version is based on the divider-and-conquer idea, and mainly includes two stages, i.e. geometry decomposition and Mesh Generation. Both stages are parallelized separately. A highly efficient fine-grain level parallel scheme is presented to parallelize the stage of geometry decomposition. A SubDomain Graph (SDG), which represents the connections of subdomains, is constructed. The task of parallel Mesh Generation is then reduced to that of the SDG partitioning. Since the number of elements in subdomains could be pre-computed before Meshing, a static load balancing scheme to partition the SDG performs well with the aid of Metis tools. Numerical results show that scalable timing performance could be achieved by using the parallel Mesh generator with resulting Meshes nicely partitioned among processors, which enables a fast parallel simulation environment by eliminating the traditional I/O-busy process of Mesh repartitioning.
Bharat K Soni - One of the best experts on this subject based on the ideXlab platform.
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octree based reasonable quality hexahedral Mesh Generation using a new set of refinement templates
International Journal for Numerical Methods in Engineering, 2009Co-Authors: Alan M Shih, Bharat K SoniAbstract:An octree-based Mesh Generation method is proposed to create reasonable-quality, geometry-adapted unstructured hexahedral Meshes automatically from triangulated surface models without any sharp geometrical features. A new, easy-to-implement, easy-to-understand set of refinement templates is developed to perform local Mesh refinement efficiently even for concave refinement domains without creating hanging nodes. A buffer layer is inserted on an octree core Mesh to improve the Mesh quality significantly. Laplacian-like smoothing, angle-based smoothing and local optimization-based untangling methods are used with certain restrictions to further improve the Mesh quality. Several examples are shown to demonstrate the capability of our hexahedral Mesh Generation method for complex geometries. Copyright © 2008 John Wiley & Sons, Ltd.
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parallel unstructured Mesh Generation by an advancing front method
Mathematics and Computers in Simulation, 2007Co-Authors: Yasushi Ito, Alan M Shih, Bharat K Soni, Andrey N Chernikov, Nikos Chrisochoides, Anil K Erukala, Kazuhiro NakahashiAbstract:Mesh Generation is a critical step in high fidelity computational simulations. High-quality and high-density Meshes are required to accurately capture the complex physical phenomena. A robust approach for a parallel framework has been developed to generate large-scale Meshes in a short period of time. A coarse tetrahedral Mesh is generated first to provide the basis of block interfaces and then is partitioned into a number of sub-domains using METIS partitioning algorithms. A volume Mesh is generated on each sub-domain in parallel using an advancing front method. Dynamic load balancing is achieved by evenly distributing work among the processors. All the sub-domains are combined to create a single volume Mesh. The combined volume Mesh can be smoothed to remove the artifacts in the interfaces between sub-domains. A void region is defined inside each sub-domain to reduce the data points during the smoothing operation. The scalability of the parallel Mesh Generation is evaluated to quantify the improvement on shared- and distributed-memory computer systems.
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unstructured Mesh Generation using megg3d mixed element grid generator in three dimensions
2007Co-Authors: Yasushi Ito, Alan M Shih, Bharat K SoniAbstract:An efficient and robust unstructured Mesh generator, Mixed-Element Grid Generator in 3 Dimensions (MEGG3D), has been developed [-]. MEGG3D has five key components: (1) a direct advancing front method for surface triangulation based on discrete surface models [, ]; (2) a decimation method for triangular Meshes with quality enhancement methods [] (Figure 1a); (3) an advancing front method for isotropic tetrahedral Mesh Generation []; (4) a multiple marching direction method for semi-structured near-field Mesh Generation []; (5) an octree-based unstructured hexahedral Mesh Generation method with a new set of refinement templates [] (Figure 1b). MEGG3D is previously known as EdgeEditor and has been demonstrated part of its capability for generating Meshes for complex geometries. In this paper, we will summarize the current capability of MEGG3D and show variety of Meshes for complex geometries.
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reliable isotropic tetrahedral Mesh Generation based on an advancing front method
IMR, 2004Co-Authors: Yasushi Ito, Alan M Shih, Bharat K SoniAbstract:In this paper, we propose a robust isotropic tetrahedral Mesh Generation method. An advancing front method is employed to control local Mesh density and to easily preserve the original connectivity of boundary surfaces. Tetrahedra are created by each layer. Instead of preparing a background Mesh for Mesh spacing control, this information is estimated at the beginning of each layer at each node from the area of connecting triangles on the front and a user-specified stretching factor. An alternating digital tree (ADT) is prepared to correct the Mesh spacing information and to perform geometric search efficiently. At the end of the Mesh Generation process, angle-based smoothing and Delaunay refinement are employed to enhance the resulting Mesh quality. Surface Meshes are prepared beforehand using a direct advancing front method for discrete surfaces extracted from computed tomography (CT) or magnetic resonance imaging (MRI) data. The algorithm is demonstrated with several biomedical models.
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a concise representation of geometry suitable for Mesh Generation
IMR, 2002Co-Authors: Paul L Chew, Stephen A Vavasis, Sankarappan Gopalsamy, Bharat K SoniAbstract:We describe a new geometric representation scheme suitable for finite element Mesh Generation. The representation is by boundaries (i.e., brep) and relations between boundaries are stored as a directed acyclic graph. The geometry itself is based on NURBS curves and surfaces. The new geometry proposal has been been adopted by the CornellMississippi State joint ITR project. We describe why the geometric representation scheme is well-suited for Mesh Generation and engineering analysis.
Justin G Laughlin - One of the best experts on this subject based on the ideXlab platform.
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an open source Mesh Generation platform for biophysical modeling using realistic cellular geometries
Biophysical Journal, 2020Co-Authors: Justin G Laughlin, John B Moody, Rommie E Amaro, Andrew J Mccammon, Michael Holst, Padmini RangamaniAbstract:Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric Mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this work, we outline the steps for a naive user to approach the Geometry-preserving Adaptive MeshER software version 2, a Mesh Generation code written in C++ designed to convert structural data sets to realistic geometric Meshes while preserving the underlying shapes. We present two example cases: 1) Mesh Generation at the subcellular scale as informed by electron tomography and 2) Meshing a protein with a structure from x-ray crystallography. We further demonstrate that the Meshes generated by the Geometry-preserving Adaptive MeshER software are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric Meshes from structural biology data.
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an open source Mesh Generation platform for biophysical modeling using realistic cellular geometries
bioRxiv, 2019Co-Authors: Justin G Laughlin, John B Moody, Rommie E Amaro, Andrew J Mccammon, Michael Holst, Padmini RangamaniAbstract:ABSTRACT Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric Mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a naive user to approach GAMer 2, a Mesh Generation code written in C++ designed to convert structural datasets to realistic geometric Meshes, while preserving the underlying shapes. We present two example cases, 1) Mesh Generation at the subcellular scale as informed by electron tomography, and 2) Meshing a protein with structure from x-ray crystallography. We further demonstrate that the Meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric Meshes from structural biology data. SIGNIFICANCE As biophysical structure determination methods improve, the rate of new structural data is increasing. New methods that allow the interpretation, analysis, and reuse of such structural information will thus take on commensurate importance. In particular, geometric Meshes, such as those commonly used in graphics and mathematics, can enable a myriad of mathematical analysis. In this work, we describe GAMer 2, a Mesh Generation library designed for biological datasets. Using GAMer 2 and associated tools PyGAMer and BlendGAMer, biologists can robustly generate computer and algorithm friendly geometric Mesh representations informed by structural biology data. We expect that GAMer 2 will be a valuable tool to bring realistic geometries to biophysical models.
Jonathan Richard Shewchuk - One of the best experts on this subject based on the ideXlab platform.
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delaunay Mesh Generation
2012Co-Authors: Siuwing Cheng, Tamal K Dey, Jonathan Richard ShewchukAbstract:Written by authors at the forefront of modern algorithms research, Delaunay Mesh Generation demonstrates the power and versatility of Delaunay Meshers in tackling complex geometric domains ranging from polyhedra with internal boundaries to piecewise smooth surfaces. Covering both volume and surface Meshes, the authors fully explain how and why these Meshing algorithms work. The book is one of the first to integrate a vast amount of cutting-edge material on Delaunay triangulations. It begins with introducing the problem of Mesh Generation and describing algorithms for constructing Delaunay triangulations. The authors then present algorithms for generating high-quality Meshes in polygonal and polyhedral domains. They also illustrate how to use restricted Delaunay triangulations to extend the algorithms to surfaces with ridges and patches and volumes with smooth surfaces. For researchers and graduate students, the book offers a rigorous theoretical analysis of Mesh Generation methods. It provides the necessary mathematical foundations and core theoretical results upon which researchers can build even better algorithms in the future. For engineers, the book shows how the algorithms work well in practice. It explains how to effectively implement them in the design and programming of Mesh Generation software.
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anisotropic voronoi diagrams and guaranteed quality anisotropic Mesh Generation
Symposium on Computational Geometry, 2003Co-Authors: Francois Labelle, Jonathan Richard ShewchukAbstract:We introduce anisotropic Voronoi diagrams, a generalization of multiplicatively weighted Voronoi diagrams suitable for generating guaranteed-quality Meshes of domains in which long, skinny triangles are required, and where the desired anisotropy varies over the domain. We discuss properties of anisotropic Voronoi diagrams of arbitrary dimensionality---most notably circumstances in which a site can see its entire Voronoi cell. In two dimensions, the anisotropic Voronoi diagram dualizes to a triangulation under these same circumstances. We use these properties to develop an algorithm for anisotropic triangular Mesh Generation in which no triangle has an angle smaller than 20A, as measured from the skewed perspective of any point in the triangle.
