3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Numerical and experimental design study of a regenerative pump

This paper presents the use of a commercial CFD code to simulate the flow-field within the regenerative pump and compare the CFD results with new experimental data. Regenerative pumps are the subject of increased interest in industry as these pumps are low cost, low specific speed, compact and able to deliver high heads with stable performance characteristics. The complex flow-field within the regenerative pump represents a considerable challenge to detailed mathematical modelling. This paper also presents a novel rapid manufacturing process used to consider the effect of impeller geometry changes on the pump efficiency. Ten modified impeller blade profiles, relative to a standard radial configuration, were evaluated. The CFD performance results demonstrate reasonable agreement with the experimental tests. The CFD results also demonstrate that it is possible to represent the helical flow field for the pump which has been witnessed only in experimental flow visualisation until now. The ability to use CFD modelling in conjunction with rapid manufacturing techniques has meant that more complex impeller geometry configurations can now be assessed with better understanding of the flow-field and resulting efficiency

Study of a regenerative pump using numerical and experimental techniques

Regenerative pumps are the subject of increased interest in industry as these pumps are low cost, low specific speed, compact and able to deliver high heads with stable performance characteristics. The complex flow-field within the pump represents a considerable challenge to detailed mathematical modelling as there is significant flow separation in the impeller blading. This paper presents the use of a commercial CFD code to simulate the flow within the regenerative pump and compare the CFD results with new experimental data. The CFD results demonstrate that it is possible to represent the helical flowfield for the pump which has only been witnessed in experimental flow visualisation until now. The CFD performance results also demonstrate reasonable agreement with the experimental tests. The CFD models are currently being used to optimise key geometric features to increase pump efficiency

Design optimisation of a regenerative pump using numerical and experimental techniques

Regenerative pumps are the subject of increased interest in industry as these pumps are low cost, low specific speed, compact and able to deliver high heads with stable performance characteristics. The complex flow-field within the pump represents a considerable challenge to detailed mathematical modelling. This paper outlines the use of a commercial CFD code to simulate the flow-field within the regenerative pump and compare the CFD results with new experimental data. A novel rapid manufacturing process is used to consider the effect of impeller geometry changes on the pump efficiency. The CFD results demonstrate that it is possible to represent the helical flow field for the pump which has only been witnessed in experimental flow visualisation until now. The CFD performance results also demonstrate reasonable agreement with the experimental tests. The ability to use CFD modelling in conjunction with rapid manufacturing techniques has meant that more complex impeller geometry configurations can now be assessed with better understanding of the flow-field and resulting efficiency

Finite Element Based Tracking of Deforming Surfaces

We present an approach to robustly track the geometry of an object that deforms over time from a set of input point clouds captured from a single viewpoint. The deformations we consider are caused by applying forces to known locations on the object's surface. Our method combines the use of prior information on the geometry of the object modeled by a smooth template and the use of a linear finite element method to predict the deformation. This allows the accurate reconstruction of both the observed and the unobserved sides of the object. We present tracking results for noisy low-quality point clouds acquired by either a stereo camera or a depth camera, and simulations with point clouds corrupted by different error terms. We show that our method is also applicable to large non-linear deformations.Comment: additional experiment

Finite element model creation and stability considerations of complex biological articulation : the human wrist joint

The finite element method has been used with considerable success to simulate the behaviour of various joints such as the hip, knee and shoulder. It has had less impact on more complicated joints such as the wrist and the ankle. Previously published finite element studies on these multi bone joints have needed to introduce un-physiological boundary conditions in order to establish numerical convergence of the model simulation. That is necessary since the stabilising soft tissue mechanism of these joints is usually too elaborate in order to be fully included both anatomically and with regards to material properties. This paper looks at the methodology of creating a finite element model of such a joint focussing on the wrist and the effects additional constraining has on the solution of the model. The study shows that by investigating the effects each of the constraints, a better understanding on the nature of the stabilizing mechanisms of these joints can be achieved

Three Dimensional Electrical Impedance Tomography

The electrical resistivity of mammalian tissues varies widely and is correlated with physiological function. Electrical impedance tomography (EIT) can be used to probe such variations in vivo, and offers a non-invasive means of imaging the internal conductivity distribution of the human body. But the computational complexity of EIT has severe practical limitations, and previous work has been restricted to considering image reconstruction as an essentially two-dimensional problem. This simplification can limit significantly the imaging capabilities of EIT, as the electric currents used to determine the conductivity variations will not in general be confined to a two-dimensional plane. A few studies have attempted three-dimensional EIT image reconstruction, but have not yet succeeded in generating images of a quality suitable for clinical applications. Here we report the development of a three-dimensional EIT system with greatly improved imaging capabilities, which combines our 64-electrode data-collection apparatus with customized matrix inversion techniques. Our results demonstrate the practical potential of EIT for clinical applications, such as lung or brain imaging and diagnostic screening

Scalable generation of large-scale unstructured meshes by a novel domain decomposition approach

© 2018 Elsevier Ltd A parallel algorithm is proposed for scalable generation of large-scale tetrahedral meshes. The key innovation is the use of a mesh-simplification based domain decomposition approach. This approach works on a background mesh with both its surface and its interior elements much larger than the final elements desired, and decomposes the domain into subdomains containing no undesirable geometric features in the inter-domain interfaces. In this way, the most time-consuming part of domain decomposition can be efficiently parallelized, and other sequential parts consume reasonably limited computing time since they treat a very coarse background mesh. Meanwhile, the subsequent parallel procedures of mesh generation and improvement are most efficient because they can treat individual subdomains without compromising element quality. Compared with published state-of-the-art parallel algorithms, the developed parallel algorithm can reduce the clock time required by the creation of one billion elements on 512 computer cores from roughly half an hour to less than 4 minutes