High-fidelity geometric modeling for biomedical applications

Yu, Zeyun; Holst, Michael; McCammon, J. Andrew

doi:10.1016/j.finel.2008.03.004

Cited by 47 publications

(45 citation statements)

References 51 publications

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“…The dimension of the mesh is: 1430 × 940 × 406 nm. F, the SR is divided into nine distinct compartments, 1 jSR, 2 Z-line SR mesh was improved using our previously described surface mesh improvement library GAMer (Yu et al 2008b;www.fetk.org), installed as a plug-in to Blender (www.blender.org). The improved and annotated mesh can be seen in Fig.…”

Section: Geometrymentioning

confidence: 99%

“…Automated segmentation processes should ultimately improve the efficiency of this step (Pham et al 2000;Volkmann, 2010;Helmstaedter & Mitra, 2012). We used our freely available software package GAMer (Yu et al 2008b;www.fetk.org) to imropve the quality of the segmented mesh, and to further improve the usability of GAMer, we made it available as a plugin for the graphical user interface of Blender (www.blender.org), a feely available software tool for computer graphics and animation.…”

Section: Softwarementioning

confidence: 99%

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Modelling cardiac calcium sparks in a three‐dimensional reconstruction of a calcium release unit

Hake

Edwards

et al. 2012

The Journal of Physiology

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106

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Key points• We have developed a detailed computational model of a cardiac Ca 2+ spark based on a three dimensional reconstruction of electron tomograms.• Our model predicts near total junctional Ca 2+ depletion after the spark, while regional Ca 2+ reserve is preserved. The local Ca 2+ gradient inferred by these findings reconciles previous model predictions with experimental measurements.• Differences in local distribution of calsequestrin have a profound impact on spark termination time, as reported by Fluo5, solely based on its Ca 2+ buffering capacity.• The SERCA pump can prolong spark release time by pumping Ca 2+ back into the junctional SR during the spark. Abstract Triggered release of Ca2+ from an individual sarcoplasmic reticulum (SR) Ca 2+ release unit (CRU) is the fundamental event of cardiac excitation-contraction coupling, and spontaneous release events (sparks) are the major contributor to diastolic Ca 2+ leak in cardiomyocytes. Previous model studies have predicted that the duration and magnitude of the spark is determined by the local CRU geometry, as well as the localization and density of Ca 2+ handling proteins. We have created a detailed computational model of a CRU, and developed novel tools to generate the computational geometry from electron tomographic images. Ca 2+ diffusion was modelled within the SR and the cytosol to examine the effects of localization and density of the Na + /Ca 2+ exchanger, sarco/endoplasmic reticulum Ca 2+ -ATPase 2 (SERCA), and calsequestrin on spark dynamics. We reconcile previous model predictions of approximately 90% local Ca 2+ depletion in junctional SR, with experimental reports of about 40%. This analysis supports the hypothesis that dye kinetics and optical averaging effects can have a significant impact on measures of spark dynamics. Our model also predicts that distributing calsequestrin within non-junctional Z-disc SR compartments, in addition to the junctional compartment, prolongs spark release time as reported by Fluo5. By pumping Ca 2+ back into the SR during a release, SERCA is able to prolong a Ca 2+ spark, and this may contribute to SERCA-dependent changes in Ca 2+ wave speed. Finally, we show that including the Na + /Ca 2+ exchanger inside the dyadic cleft does not alter local [Ca 2+ ] during a spark.

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Section: Geometrymentioning

confidence: 99%

Section: Softwarementioning

confidence: 99%

Modelling cardiac calcium sparks in a three‐dimensional reconstruction of a calcium release unit

Hake

Edwards

et al. 2012

The Journal of Physiology

Self Cite

106

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“…In 2006, Zhang et al [26] used a modified dual contouring method to generate meshes for biomolecular structures. A later tool, GAMer [27,28], was developed for improving the qualities of the meshes of Gaussian surface produced by marching cubes method.…”

Section: Some Definitions and Meshing Methods For Molecular Surfacementioning

confidence: 99%

Advances in biomolecular surface meshing and its applications to mathematical modeling

Chen

2013

Chin. Sci. Bull.

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In the field of molecular modeling and simulation, molecular surface meshes are necessary for many problems, such as molecular structure visualization and analysis, docking problem and implicit solvent modeling and simulation. Recently, with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation, providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure. In this review, we summarize recent works on this issue. First, various definitions of molecular surfaces and corresponding meshing methods are introduced. Second, our recent meshing tool, TMSmesh, and its performances are presented. Finally, we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM). molecular surface meshing, manifold mesh, mathematical modeling, TMSmeshCitation: Chen M X, Lu B Z. Advances in biomolecular surface meshing and its applications to mathematical modeling. Chin Sci Bull, 2013Bull, , 58: 1843Bull, -1849 10.1007/s11434-013-5829-8One main goal of computational structural biology/chemistry is to understand the functions and mechanisms of biomolecular systems and their relations to molecular structures with a wide range of computational approaches. To achieve this, proper and correct representation of the interface between biomolecule and solvent, molecular surface, is a primary task. In the field of implicit solvent modeling and continuum modeling, the molecular surface is used to model the dielectric interface which is the transition from the low-dielectric solute region to the high-dielectric solvent region. It is also important and useful in materials science and surface science [1]. Meshing molecular surface is a prerequisite for using boundary element method (BEM) and finite element method (FEM) in the implicit solvent models, and it is a more demanding task than for the only purposes of visualization and/or geometry analyses of molecular structure. So far, due to the highly complex and irregular shape of the molecular surface, *Corresponding author (email: bzlu@lsec.cc.ac.cn) efficient meshing of molecular surface for large real biomolecule with high quality remains a challenging problem. Actually, it was historically a great impediment to use BEM/FEM in continuum modeling of large molecular systems.The main purpose of this paper is to review the various definitions and meshing methods for molecular surface, including our recent work, and introduce their applications in implicit solvent modeling and simulation. Following this introduction section, in Section 1, various definitions of molecular surfaces and corresponding meshing methods are introduced. In Section 2, our recent algorithm and software, TMSmesh, are focused. We also made comparisons with some other methods. In Section 3, a closely related topic, volume me...

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“…In order to provide a patient-specific simulation, accurate geometric modeling of the target area is required. A lot of work has been done to create a geometric model from medical images for use in simulations [23,24]. While there is a push to automate this part of the process, significant user input is still required for proper classification and segmentation.…”

Section: Background and Related Workmentioning

confidence: 99%

Estimating an equivalent wall-thickness of a cerebral aneurysm through surface parameterization and a non-linear spring system

Johnson

Zhang

Shimada

2010

Int. J. Numer. Meth. Biomed. Engng.

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SUMMARYCerebral aneurysms are an enlargement of a brain blood-vessel due to a weakened wall and can pose significant health risks. Computational simulations have been thus utilized to help doctors in the understanding of cerebral aneurysms. In order to provide more accurate patient-specific simulations, not only does geometry for the fluid domain need to be created from medical image data, but more accurate wall-models need to be generated as well. However, the wall-thickness and material properties are very difficult to obtain experimentally, and thus most computational simulations, except for a few we have seen in the recent years, are performed using walls with uniform thickness and constant material properties. To provide a more accurate computational model for the weakened wall-structure, this paper presents a novel estimation of an equivalent cerebral aneurysm wall-thickness by deforming a healthy vessel onto an aneurysm through surface parameterization and a non-linear spring system. The resulting wall-model is thinnest over the dome of the aneurysm, and for the patient-specific models used has an average thickness of 75 m. Fluid-structure interaction simulations of three patient-specific cerebral aneurysms are carried out. Compared with using a uniform wall-thickness, using the equivalent wall-thickness gives a more accurate prediction of the rupture site.

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High-fidelity geometric modeling for biomedical applications

Cited by 47 publications

References 51 publications

Modelling cardiac calcium sparks in a three‐dimensional reconstruction of a calcium release unit

Modelling cardiac calcium sparks in a three‐dimensional reconstruction of a calcium release unit

Advances in biomolecular surface meshing and its applications to mathematical modeling

Estimating an equivalent wall-thickness of a cerebral aneurysm through surface parameterization and a non-linear spring system

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