58,090 research outputs found
Unsupervised cryo-EM data clustering through adaptively constrained K-means algorithm
In single-particle cryo-electron microscopy (cryo-EM), K-means clustering
algorithm is widely used in unsupervised 2D classification of projection images
of biological macromolecules. 3D ab initio reconstruction requires accurate
unsupervised classification in order to separate molecular projections of
distinct orientations. Due to background noise in single-particle images and
uncertainty of molecular orientations, traditional K-means clustering algorithm
may classify images into wrong classes and produce classes with a large
variation in membership. Overcoming these limitations requires further
development on clustering algorithms for cryo-EM data analysis. We propose a
novel unsupervised data clustering method building upon the traditional K-means
algorithm. By introducing an adaptive constraint term in the objective
function, our algorithm not only avoids a large variation in class sizes but
also produces more accurate data clustering. Applications of this approach to
both simulated and experimental cryo-EM data demonstrate that our algorithm is
a significantly improved alterative to the traditional K-means algorithm in
single-particle cryo-EM analysis.Comment: 35 pages, 14 figure
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
Nanoscale mosaicity revealed in peptide microcrystals by scanning electron nanodiffraction.
Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nanocrystals requires assumptions of bulk crystallinity and domain block substructure. Here we map lattice structure across micron size areas of cryogenically preserved three-dimensional peptide crystals using a nano-focused electron beam. This approach produces diffraction from as few as 1500 molecules in a crystal, is sensitive to crystal thickness and three-dimensional lattice orientation. Real-space maps reconstructed from unsupervised classification of diffraction patterns across a crystal reveal regions of crystal order/disorder and three-dimensional lattice tilts on the sub-100nm scale. The nanoscale lattice reorientation observed in the micron-sized peptide crystal lattices studied here provides a direct view of their plasticity. Knowledge of these features facilitates an improved understanding of peptide assemblies that could aid in the determination of structures from nano- and microcrystals by single or serial crystal electron diffraction
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