Point-cloud method for image-based biomechanical stress analysis

Qian, Jing; Lu, Jia

doi:10.1002/cnm.1432

Cited by 7 publications

(3 citation statements)

References 33 publications

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“…The use of a point-cloud method (a form of meshfree method based on the nodal discretization of a problem domain) for image-based stress analysis in biological systems, such as aorta inflation and skull impact, was demonstrated by Qian and Lu [311]. A 3D material point human head model constructed from CT scanned images was used to study the dynamic response of the human head under the impact of a 3D cylindrical lead projectile [312], while the penetration of projectile into the human head was studied using SPH method [313].…”

Section: Other Applicationsmentioning

confidence: 99%

Meshfree and Particle Methods in Biomechanics: Prospects and Challenges

Zhang

Ademiloye

Liew

2018

Arch Computat Methods Eng

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The use of meshfree and particle methods in the field of bioengineering and biomechanics has significantly increased. This may be attributed to their unique abilities to overcome most of the inherent limitations of mesh-based methods in dealing with problems involving large deformation and complex geometry that are common in bioengineering and computational biomechanics in particular. This review article is intended to identify, highlight and summarize research works on topics that are of substantial interest in the field of computational biomechanics in which meshfree or particle methods have been employed for analysis, simulation or/and modeling of biological systems such as soft matters, cells, biological soft and hard tissues and organs. We also anticipate that this review will serve as a useful resource and guide to researchers who intend to extend their work into these research areas. This review article includes 333 references. Highlights  We present an up to date review of meshfree and particle methods, including their advantages and limitations.  We comprehensively discuss past and recent applications of meshfree and particle methods in bioengineering and biomechanics.  We identify research areas, directions, and opportunities for the application of meshfree and particle methods in bioengineering and biomechanics.

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Section: Other Applicationsmentioning

confidence: 99%

Meshfree and Particle Methods in Biomechanics: Prospects and Challenges

Zhang

Ademiloye

Liew

2018

Arch Computat Methods Eng

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“…With a given surface, the surface meshing and volumetric meshing [67, 24] are important tasks as in the continuum mechanical analysis [56, 59, 65]. Many elegant methods have been developed, including such as the probabilistic methods for centroidal Voronoi tessellations [26, 45], the optimal Delaunay triangulation and graph cut based variational surface reconstruction [72], and other surface remeshing enhancement methods and technologies [68, 64, 67, 73, 37], to generate high quality triangle surface meshes that are low-noise, low memory cost, near 60° for majority of element angles and aligned with the physical features.…”

Section: Introductionmentioning

confidence: 99%

Multiscale geometric modeling of macromolecules II: Lagrangian representation

et al. 2013

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Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X-ray, NMR and cryo-EM, and theoretical/mathematical models, such as molecular dynamics, the Poisson-Boltzmann equation and the Nernst-Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger’s functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent-solute interaction, and ion channel dynamics, while our coarse resolution representations highlight the compatibility of protein-ligand bindings and possibility of protein-protein interactions.

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“…There are a wide variety of methods that can be used for this purpose. Mesh generation is one of the most important aspects of continuum mechanical analysis [59][60][61][62][63]. Numerous elegant methods, such as the probabilistic methods for centroidal Voronoi tessellations [64,65], the optimal Delaunay triangulation and graph cut-based variational surface reconstruction [66], and other surface remeshing enhancement methods and technologies [41,[67][68][69][70], have been developed for surface reconstruction or surface remeshing during the past two decades.…”

Section: Introductionmentioning

confidence: 99%

Geometric modeling of subcellular structures, organelles, and multiprotein complexes

Feng

Xia

Tong

et al. 2012

Numer Methods Biomed Eng

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SUMMARY Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes.

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Point-cloud method for image-based biomechanical stress analysis

Cited by 7 publications

References 33 publications

Meshfree and Particle Methods in Biomechanics: Prospects and Challenges

Meshfree and Particle Methods in Biomechanics: Prospects and Challenges

Multiscale geometric modeling of macromolecules II: Lagrangian representation

Geometric modeling of subcellular structures, organelles, and multiprotein complexes

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