Frontiers in biomolecular mesh generation and molecular visualization systems

Gui, Sheng; Khan, Dawar; Wang, Qin; Yan, Dong‐Ming; Lu, Benzhuo

doi:10.1186/s42492-018-0007-0

Cited by 8 publications

(5 citation statements)

References 111 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There are various kinds of definitions for a molecular surface, 51 including the van der Waals surface (VDWs), the solvent-accessible surface (SAS), 52 the solvent-excluded surface (SES), 53 etc.…”

Section: Unfitted Mesh and Interface Resolutionmentioning

confidence: 99%

An Unfitted Finite Element Poisson–Boltzmann Solver with Automatic Resolving of Curved Molecular Surface

Liu,

Gui,

et al. 2024

J. Phys. Chem. B

Self Cite

View full text Add to dashboard Cite

So far, the existing Poisson−Boltzmann (PB) solvers that accurately take into account the interface jump conditions need a pregenerated body-fitted mesh (molecular surface mesh). However, qualified biomolecular surface meshing and its implementation into numerical methods remains a challenging and laborious issue, which practically hinders the progress of further developments and applications of a bunch of numerical methods in this field. In addition, even with a molecular surface mesh, it is only a low-order approximation of the original curved surface. In this article, an interface-penalty finite element method (IPFEM), which is a typical unfitted finite element method, is proposed to solve the Poisson−Boltzmann equation (PBE) without requiring the user to generate a molecular surface mesh. The Gaussian molecular surface is used to represent the molecular surface and can be automatically resolved with a high-order approximation within our method. Theoretical convergence rates of the IPFEM for the linear PB equation have been provided and are well validated on a benchmark problem with an analytical solution (we also noticed from numerical examples that the IPFEM has similar convergence rates for the nonlinear PBE). Numerical results on a set of different-sized biomolecules demonstrate that the IPFEM is numerically stable and accurate in the calculation of biomolecular electrostatic solvation energy.

show abstract

Section: Unfitted Mesh and Interface Resolutionmentioning

confidence: 99%

An Unfitted Finite Element Poisson–Boltzmann Solver with Automatic Resolving of Curved Molecular Surface

Liu,

Gui,

et al. 2024

J. Phys. Chem. B

Self Cite

View full text Add to dashboard Cite

show abstract

“…Based on their goals, their study [14] is related to ours; however, their review is not clearly defined and is specific to SR remeshing. There have been some other surveys covering only a specific meshing domain, such as unstructured meshes [15], feature remeshing [16], bio-medical mesh generation [17], and molecular surface meshing [18]. Araújo et al [19] conducted a comprehensive survey on implicit surfaces (IS) and visualization methods.…”

Section: Related Surveysmentioning

confidence: 99%

“…In this way, they proposed a new CVT-based method for quality surface remeshing, avoiding small and obtuse angles. The improved energy function is given in Equations ( 17) and (18). The angle bound is [30 o , 90 o ], and the vertex regularity for V 567% is near to 100.…”

Section: Centroidal Voronoi Tessellation (Cvt)mentioning

confidence: 99%

Surface Remeshing: A Systematic Literature Review of Methods and Research Directions

Khan

Plopski

Fujimoto

et al. 2022

IEEE Trans. Visual. Comput. Graphics

Self Cite

View full text Add to dashboard Cite

Triangle meshes are used in many important shape-related applications including geometric modeling, animation production, system simulation, and visualization. However, these meshes are typically generated in raw form with several defects and poor-quality elements, obstructing them from practical application. Over the past decades, different surface remeshing techniques have been presented to improve these poor-quality meshes prior to the downstream utilization. A typical surface remeshing algorithm converts an input mesh into a higher quality mesh with consideration of given quality requirements as well as an acceptable approximation to the input mesh. In recent years, surface remeshing has gained significant attention from researchers and engineers, and several remeshing algorithms have been proposed. However, there has been no survey article on remeshing methods in general with a defined search strategy and article selection mechanism covering the recent approaches in surface remeshing domain with a good connection to classical approaches. In this article, we present a survey on surface remeshing techniques, classifying all collected articles in different categories and analyzing specific methods with their advantages, disadvantages, and possible future improvements. Following the systematic literature review methodology, we define step-by-step guidelines throughout the review process, including search strategy, literature inclusion/exclusion criteria, article quality assessment, and data extraction. With the aim of literature collection and classification based on data extraction, we summarized collected articles, considering the key remeshing objectives, the way the mesh quality is defined and improved, and the way their techniques are compared with other previous methods. Remeshing objectives are described by angle range control, feature preservation, error control, valence optimization, and remeshing compatibility. The metrics used in the literature for the evaluation of surface remeshing algorithms are discussed. Meshing techniques are compared with other related methods via a comprehensive table with indices of the method name, the remeshing challenge met and solved, the category the method belongs to, and the year of publication. We expect this survey to be a practical reference for surface remeshing in terms of literature classification, method analysis, and future prospects.

show abstract

“…Initially, this smoothing scheme starts with the projection of each vertex onto the fitted surface. For a detailed study of molecular mesh generation and molecular visualization, please refer to the recent survey paper [34]. The curvature is used to label all the vertices into four categories.…”

Section: Related Workmentioning

confidence: 99%

Valence optimization and angle improvement for molecular surface remeshing

et al. 2020

Self Cite

View full text Add to dashboard Cite

Molecular surface mesh generation plays a vital role in molecular modeling and visualization. However, meshes extracted directly from Protein Data Bank files have several issues such as small and large triangles, redundant elements, selfintersections, and irregular vertices. The state-of-the-art mesh improvement methods often fail to deal with these issues. In this paper, we present a novel method for valence optimization and angle improvement. For valence optimization, we remove the bad valence vertices with its neighbor triangle making regular holes in the mesh. The holes are filled in a careful manner to improve their valences as well as angle quality. We also use a segmentation-based surface remeshing which segments the mesh into random segments and then each segment is independently remeshed. In addition, a point insertion scheme is applied to minimize the ratio of obtuse triangles. Experimental results show that our method not only improves the maximal and minimal angles to an angle bound of [30 • 120 • ] but also improves the vertices' regularity, reduces the ratio of obtuse triangles, preserves the area and volume, and always succeeds with downstream applications.

show abstract

Frontiers in biomolecular mesh generation and molecular visualization systems

Cited by 8 publications

References 111 publications

An Unfitted Finite Element Poisson–Boltzmann Solver with Automatic Resolving of Curved Molecular Surface

An Unfitted Finite Element Poisson–Boltzmann Solver with Automatic Resolving of Curved Molecular Surface

Surface Remeshing: A Systematic Literature Review of Methods and Research Directions

Valence optimization and angle improvement for molecular surface remeshing

Contact Info

Product

Resources

About