Robust multi-view L2 triangulation via optimal inlier selection and 3D structure refinement

2014 ◽  
Vol 47 (9) ◽  
pp. 2974-2992 ◽  
Author(s):  
Lai Kang ◽  
Lingda Wu ◽  
Yee-Hong Yang
Keyword(s):  
Structure Refinement ◽  
3D Structure ◽  
Inlier Selection

Quantitative structure determination of interfaces through Z-contrast imaging and electron energy loss spectroscopy

1996 ◽  
Vol 54 ◽  
pp. 104-105
Author(s):  
S. J. Pennycook ◽  
P. D. Nellist ◽  
N. D. Browning ◽  
P. A. Langjahr ◽  
M. Rühle
Keyword(s):  
Grain Boundaries ◽  
Cuprate Superconductors ◽  
Structure Refinement ◽  
3D Structure ◽  
Real Space ◽  
Contrast Imaging ◽  
Coordination Polyhedra ◽  
Burgers Vector ◽  
Z Contrast ◽  
Contrast Image

The simultaneous use of Z-contrast imaging with parallel detection EELS in the STEM provides a powerful means for determining the atomic structure of grain boundaries. The incoherent Z-contrast image of the high atomic number columns can be directly inverted to their real space arrangement, without the use of preconceived structure models. Positions and intensities may be accurately quantified through a maximum entropy analysis. Light elements that are not visible in the Z-contrast image can be studied through EELS; their coordination polyhedra determined from the spectral fine structure. It even appears feasible to contemplate 3D structure refinement through multiple scattering calculations.The power of this approach is illustrated by the recent study of a series of SrTiC>3 bicrystals, which has provided significant insight into some of the basic issues of grain boundaries in ceramics. Figure 1 shows the structural units deduced from a set of 24°, 36° and 65° symmetric boundaries, and 24° and 45° asymmetric boundaries. It can be seen that apart from unit cells and fragments from the perfect crystal, only three units are needed to construct any arbitrary tilt boundary. For symmetric boundaries, only two units are required, each having the same Burgers, vector of a<100>. Both units are pentagons, on either the Sr or Ti sublattice, and both contain two columns of the other sublattice, imaging in positions too close for the atoms in each column to be coplanar. Each column was therefore assumed to be half full, with the pair forming a single zig-zag column. For asymmetric boundaries, crystal geometry requires two types of dislocations; the additional unit was found to have a Burgers’ vector of a<110>. Such a unit is a larger source of strain, and is especially important to the transport characteristics of cuprate superconductors. These zig-zag columns avoid the problem of like-ion repulsion; they have also been seen in TiO2 and YBa2Cu3O7-x and may be a general feature of ionic materials.

Monocular Structure from Motion Based on Angular BA

2015 ◽  
Vol 742 ◽  
pp. 290-293
Author(s):  
Xiu Zhi Li ◽  
Ai Lin Yang ◽  
Huan Qiu ◽  
Song Min Jia
Keyword(s):  
Optical Flow ◽  
Structure From Motion ◽  
Structure Refinement ◽  
3D Structure ◽  
Flow Fields ◽  
Image Point ◽  
Pixel Pair ◽  
Pair Matching ◽  
Dense Correspondence

This paper presents a technique for monocular Structure from Motion (SFM) that reconstructs 3D world shape. The technique proposed uses optical flow for 2D pixel pair matching and Angular Bundle Ajustment (ABA) for 3D structure refinement. The proposed strategy has two main advantages. Firstly, optical flow fields provide sufficient dense correspondence of image point pairs and secondly, ABA outperforms classic BA variants, especially for the points relatively far from camera. The reconstruction results obtained in realistic scenario demonstrate the effectiveness and accuracy of the proposed algorithm.

scholarly journals Spring Model – chromatin modeling tool based on OpenMM

2019 ◽  
Author(s):  
Michal Kadlof ◽  
Julia Rozycka ◽  
Dariusz Plewczynski
Keyword(s):  
Local Density ◽  
Structure Refinement ◽  
3D Structure ◽  
Data Bank ◽  
Chromatin Domain ◽  
Initial Structure ◽  
Domain Modeling ◽  
Building Models ◽  
Spherical Container ◽  
The Impact

AbstractChromatin structures modelling is a rapidly developing field. Parallel to the enormous growth of available experimental data, there is a growing need of building and visualizing 3D structures of nuclei, chromosomes, chromatin domains, and single loops associated with particular genes locus. Here we present a tool for chromatin domain modeling. It is available as a webserver and standalone python script. Our tool is based on molecular mechanics. It uses OpenMM engine for building models. In this method, the user has to provide contacts and will obtain 3D structure that satisfies these contacts. Additional extra parameters allow controlling fibre stiffness, type of initial structure, resolution. There are also options for structure refinement, and modelling in a spherical container. A user may provide contacts using beads indices, or paste interactions in genome coordinates from BEDPE file. After modelling user is able to download the structure in Protein Data Bank (PDB) file format for further analysis.We dedicate this tool for all who are interested in chromatin structures. It is suitable for quick visualization of datasets, studying the impact of structural variants (SVs), inspecting the effects of adding and removing particular contacts, measuring features like maximum distances between certain sites (e.g. promotor-enhancer) or local density of chromatin.

scholarly journals i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e69648 ◽  
Author(s):  
Debswapna Bhattacharya ◽  
Jianlin Cheng
Keyword(s):  
Structure Refinement ◽  
3D Structure ◽  
Protein 3D Structure

scholarly journals In silico design of a triple-negative breast cancer vaccine by targeting cancer testis antigens

Bioimpacts ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 45-56 ◽  
Author(s):  
Sepideh Parvizpour ◽  
Jafar Razmara ◽  
Mohammad M. Pourseif ◽  
Yadollah Omidi
Keyword(s):  
Breast Cancer ◽  
Cancer Vaccine ◽  
Triple Negative Breast Cancer ◽  
In Silico ◽  
Triple Negative ◽  
Structure Refinement ◽  
3D Structure ◽  
Peptide Vaccine ◽  
Dynamics Simulation ◽  
Cancer Testis

Introduction: Triple-negative breast cancer (TNBC) is an important subtype of breast cancer, which occurs in the absence of estrogen, progesterone and HER-2 receptors. According to the recent studies, TNBC may be a cancer testis antigen (CTA)-positive tumor, indicating that the CTA-based cancer vaccine can be a treatment option for the patients bearing such tumors. Of these antigens (Ags), the MAGE-A family and NY-ESO-1 as the most immunogenic CTAs are the potentially relevant targets for the development of an immunotherapeutic way of the breast cancer treatment. Methods: In the present study, immunoinformatics approach was used to design a multi-epitope peptide vaccine to combat the TNBC. The vaccine peptide was constructed by the fusion of three crucial components, including the CD8+ cytotoxic T lymphocytes (CTLs) epitopes, helper epitopes and adjuvant. The epitopes were predicted from the MAGE-A and NY-ESO-1 Ags. In addition, the granulocyte-macrophage-colony-stimulating factor (GM-CSF) was used as an adjuvant to promote the CD4+ T cells towards the T-helper for more strong induction of CTL responses. The components were conjugated by proper linkers. Results: The vaccine peptide was examined for different physiochemical characteristics to confirm the safety and immunogenic behavior. Furthermore, the 3D-structure of the vaccine peptide was predicted based on the homology modeling approach using the MODELLER v9.17 program. The vaccine structure was also subjected to the molecular dynamics simulation study for structure refinement. The results verified the immunogenicity and safety profile of the constructed vaccine as well as its capability for stimulating both the cellular and humoral immune responses. Conclusion: Based on our in-silico analyses, the proposed vaccine may be considered for the immunotherapy of TNBC.

scholarly journals GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

2019 ◽  
Vol 47 (W1) ◽  
pp. W451-W455 ◽  
Author(s):  
Gyu Rie Lee ◽  
Jonghun Won ◽  
Lim Heo ◽  
Chaok Seok
Keyword(s):  
Protein Structure ◽  
Structure Refinement ◽  
Large Fraction ◽  
3D Structure ◽  
Local Error ◽  
Optimization Approach ◽  
Structure Information ◽  
Protein Structure Refinement ◽  
Recent Developments ◽  
Related Proteins

Abstract The 3D structure of a protein can be predicted from its amino acid sequence with high accuracy for a large fraction of cases because of the availability of large quantities of experimental data and the advance of computational algorithms. Recently, deep learning methods exploiting the coevolution information obtained by comparing related protein sequences have been successfully used to generate highly accurate model structures even in the absence of template structure information. However, structures predicted based on either template structures or related sequences require further improvement in regions for which information is missing. Refining a predicted protein structure with insufficient information on certain regions is critical because these regions may be connected to functional specificity that is not conserved among related proteins. The GalaxyRefine2 web server, freely available via http://galaxy.seoklab.org/refine2, is an upgraded version of the GalaxyRefine protein structure refinement server and reflects recent developments successfully tested through CASP blind prediction experiments. This method adopts an iterative optimization approach involving various structure move sets to refine both local and global structures. The estimation of local error and hybridization of available homolog structures are also employed for effective conformation search.

The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

1983 ◽  
Vol 41 ◽  
pp. 440-441
Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch
Keyword(s):  
Crystal Packing ◽  
3D Structure ◽  
Gram Negative Bacteria ◽  
Protein Ratio ◽  
Crystal Forms ◽  
Large Molecules ◽  
Functional Studies ◽  
Voltage Dependent ◽  
Planar Membranes ◽  
Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

3-D optical transfer in excitation field synthesis microscopes

1995 ◽  
Vol 53 ◽  
pp. 64-65
Author(s):  
Vijay Krishnamurthi ◽  
Brent Bailey ◽  
Frederick Lanni
Keyword(s):  
Standing Wave ◽  
Spatial Information ◽  
3D Structure ◽  
Complete Recovery ◽  
Weighting Factor ◽  
Optical Transfer Function ◽  
Excitation Field ◽  
Optical Transfer ◽  
Set Up ◽  
Focus Plane

Excitation field synthesis (EFS) refers to the use of an interference optical system in a direct-imaging microscope to improve 3D resolution by axially-selective excitation of fluorescence within a specimen. The excitation field can be thought of as a weighting factor for the point-spread function (PSF) of the microscope, so that the optical transfer function (OTF) gets expanded by convolution with the Fourier transform of the field intensity. The simplest EFS system is the standing-wave fluorescence microscope, in which an axially-periodic excitation field is set up through the specimen by interference of a pair of collimated, coherent, s-polarized beams that enter the specimen from opposite sides at matching angles. In this case, spatial information about the object is recovered in the central OTF passband, plus two symmetric, axially-shifted sidebands. Gaps between these bands represent "lost" information about the 3D structure of the object. Because the sideband shift is equal to the spatial frequency of the standing-wave (SW) field, more complete recovery of information is possible by superposition of fields having different periods. When all of the fields have an antinode at a common plane (set to be coincident with the in-focus plane), the "synthesized" field is peaked in a narrow infocus zone.

Sign in / Sign up

Export Citation Format

Share Document