812 research outputs found
How round is a protein? Exploring protein structures for globularity using conformal mapping.
We present a new algorithm that automatically computes a measure of the geometric difference between the surface of a protein and a round sphere. The algorithm takes as input two triangulated genus zero surfaces representing the protein and the round sphere, respectively, and constructs a discrete conformal map f between these surfaces. The conformal map is chosen to minimize a symmetric elastic energy E S (f) that measures the distance of f from an isometry. We illustrate our approach on a set of basic sample problems and then on a dataset of diverse protein structures. We show first that E S (f) is able to quantify the roundness of the Platonic solids and that for these surfaces it replicates well traditional measures of roundness such as the sphericity. We then demonstrate that the symmetric elastic energy E S (f) captures both global and local differences between two surfaces, showing that our method identifies the presence of protruding regions in protein structures and quantifies how these regions make the shape of a protein deviate from globularity. Based on these results, we show that E S (f) serves as a probe of the limits of the application of conformal mapping to parametrize protein shapes. We identify limitations of the method and discuss its extension to achieving automatic registration of protein structures based on their surface geometry
A Metric for genus-zero surfaces
We present a new method to compare the shapes of genus-zero surfaces. We
introduce a measure of mutual stretching, the symmetric distortion energy, and
establish the existence of a conformal diffeomorphism between any two
genus-zero surfaces that minimizes this energy. We then prove that the energies
of the minimizing diffeomorphisms give a metric on the space of genus-zero
Riemannian surfaces. This metric and the corresponding optimal diffeomorphisms
are shown to have properties that are highly desirable for applications.Comment: 33 pages, 8 figure
Learning quadrangulated patches for 3D shape parameterization and completion
We propose a novel 3D shape parameterization by surface patches, that are
oriented by 3D mesh quadrangulation of the shape. By encoding 3D surface detail
on local patches, we learn a patch dictionary that identifies principal surface
features of the shape. Unlike previous methods, we are able to encode surface
patches of variable size as determined by the user. We propose novel methods
for dictionary learning and patch reconstruction based on the query of a noisy
input patch with holes. We evaluate the patch dictionary towards various
applications in 3D shape inpainting, denoising and compression. Our method is
able to predict missing vertices and inpaint moderately sized holes. We
demonstrate a complete pipeline for reconstructing the 3D mesh from the patch
encoding. We validate our shape parameterization and reconstruction methods on
both synthetic shapes and real world scans. We show that our patch dictionary
performs successful shape completion of complicated surface textures.Comment: To be presented at International Conference on 3D Vision 2017, 201
Feature Lines for Illustrating Medical Surface Models: Mathematical Background and Survey
This paper provides a tutorial and survey for a specific kind of illustrative
visualization technique: feature lines. We examine different feature line
methods. For this, we provide the differential geometry behind these concepts
and adapt this mathematical field to the discrete differential geometry. All
discrete differential geometry terms are explained for triangulated surface
meshes. These utilities serve as basis for the feature line methods. We provide
the reader with all knowledge to re-implement every feature line method.
Furthermore, we summarize the methods and suggest a guideline for which kind of
surface which feature line algorithm is best suited. Our work is motivated by,
but not restricted to, medical and biological surface models.Comment: 33 page
Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D
Signal transduction and cell function are governed by the spatiotemporal
organization of membrane-associated molecules. Despite significant advances in
visualizing molecular distributions by 3D light microscopy, cell biologists
still have limited quantitative understanding of the processes implicated in
the regulation of molecular signals at the whole cell scale. In particular,
complex and transient cell surface morphologies challenge the complete sampling
of cell geometry, membrane-associated molecular concentration and activity and
the computing of meaningful parameters such as the cofluctuation between
morphology and signals. Here, we introduce u-Unwrap3D, a framework to remap
arbitrarily complex 3D cell surfaces and membrane-associated signals into
equivalent lower dimensional representations. The mappings are bidirectional,
allowing the application of image processing operations in the data
representation best suited for the task and to subsequently present the results
in any of the other representations, including the original 3D cell surface.
Leveraging this surface-guided computing paradigm, we track segmented surface
motifs in 2D to quantify the recruitment of Septin polymers by blebbing events;
we quantify actin enrichment in peripheral ruffles; and we measure the speed of
ruffle movement along topographically complex cell surfaces. Thus, u-Unwrap3D
provides access to spatiotemporal analyses of cell biological parameters on
unconstrained 3D surface geometries and signals.Comment: 49 pages, 10 figure
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