VESTA 3for three-dimensional visualization of crystal, volumetric and morphology data

2011 ◽  
Vol 44 (6) ◽  
pp. 1272-1276 ◽  
Author(s):  
Koichi Momma ◽  
Fujio Izumi
Keyword(s):  
Search Algorithm ◽  
Voronoi Tessellation ◽  
Three Dimensional ◽  
Structure Parameters ◽  
Volumetric Data ◽  
Complex Molecules ◽  
Visualization System ◽  
Performance Improvements ◽  
Significant Performance

VESTAis a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version,VESTA 3, implementing new features including drawing the external morphology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices.

scholarly journals An Adaptive Geometric Search Algorithm for Macromolecular Scaffold Selection

2017 ◽  
Author(s):  
Tian Jiang ◽  
P. Douglas Renfrew ◽  
Kevin Drew ◽  
Noah Youngs ◽  
Glenn Butterfoss ◽  
...  
Keyword(s):  
Protein Design ◽  
Active Site ◽  
Metal Binding ◽  
Search Algorithm ◽  
Three Dimensional ◽  
Side Chain ◽  
Enzyme Design ◽  
Hydrogen Binding ◽  
Performance Improvements ◽  
Geometric Search

AbstractA wide variety of protein and peptidomimetic design tasks require matching functional three-dimensional motifs to potential oligomeric scaffolds. Enzyme design, for example, aims to graft active-site patterns typically consisting of 3 to 15 residues onto new protein surfaces. Identifying suitable proteins capable of scaffolding such active-site engraftment requires costly searches to identify protein folds that can provide the correct positioning of side chains to host the desired active site. Other examples of biodesign tasks that require simpler fast exact geometric searches of potential side chain positioning include mimicking binding hotspots, design of metal binding clusters and the design of modular hydrogen binding networks for specificity. In these applications the speed and scaling of geometric search limits downstream design to small patterns. Here we present an adaptive algorithm to searching for side chain take-off angles compatible with an arbitrarily specified functional pattern that enjoys substantive performance improvements over previous methods. We demonstrate this method in both genetically encoded (protein) and synthetic (peptidomimetic) design scenarios. Examples of using this method with the Rosetta framework for protein design are provided but our implementation is compatible with multiple protein design frameworks and is freely available as a set of python scripts (https://github.com/JiangTian/adaptive-geometric-search-for-protein-design).

VESTA: a three-dimensional visualization system for electronic and structural analysis

2008 ◽  
Vol 41 (3) ◽  
pp. 653-658 ◽  
Author(s):  
Koichi Momma ◽  
Fujio Izumi
Keyword(s):  
Structural Model ◽  
Three Dimensional ◽  
Electronic Energy ◽  
Oxidation States ◽  
Chemical Information ◽  
Volumetric Data ◽  
Visualization System ◽  
Cross Platform ◽  
Diffraction Patterns ◽  
Physical Quantities

A cross-platform program,VESTA, has been developed to visualize both structural and volumetric data in multiple windows with tabs.VESTArepresents crystal structures by ball-and-stick, space-filling, polyhedral, wireframe, stick, dot-surface and thermal-ellipsoid models. A variety of crystal-chemical information is extractable from fractional coordinates, occupancies and oxidation states of sites. Volumetric data such as electron and nuclear densities, Patterson functions, and wavefunctions are displayed as isosurfaces, bird's-eye views and two-dimensional maps. Isosurfaces can be colored according to other physical quantities. Translucent isosurfaces and/or slices can be overlapped with a structural model. Collaboration with external programs enables the user to locate bonds and bond angles in the `graphics area', simulate powder diffraction patterns, and calculate site potentials and Madelung energies. Electron densities determined experimentally are convertible into their Laplacians and electronic energy densities.

Design Method for Braiding Process and Structure Parameters of Three Dimensional Two-Step Tubular Braided Preform

2010 ◽  
Vol 150-151 ◽  
pp. 1613-1616
Author(s):  
Yan Gao ◽  
Jia Lu Li
Keyword(s):  
Fiber Volume Fraction ◽  
Volume Fraction ◽  
Design Method ◽  
General Structure ◽  
Three Dimensional ◽  
Structure Parameters ◽  
Fiber Volume ◽  
General Methodology ◽  
Properties Of Composites

The properties of composites reinforced by three dimensional braided preform are determined by braiding structure significantly. The main objective of this paper is to develop a general methodology for the determination of the design and analysis of three dimensional two-step braided tubular preform. The arrangement pattern of axial yarns with various finenesses is derived for the uniform braiding structure of preform, which offers a possibility for achieving preferable interior structures of braided tubular preforms. Then, the general structure parameters, including the interrelation between surface braiding angles and interior braiding angles and the fiber volume fraction, are investigated in some detail. The results derived from this paper can provide a useful method for the design of 3D two-step tubular braided preform.

scholarly journals Torsional Potential Energy Surfaces of Dinitrobenzene Isomers

2017 ◽  
Vol 2017 ◽  
pp. 1-7
Author(s):  
Paul M. Smith ◽  
Mario F. Borunda
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Basis Sets ◽  
Valuable Insight ◽  
Complex Molecules ◽  
Torsional Potential ◽  
Energy Surfaces

The torsional potential energy surfaces of 1,2-dinitrobenzene, 1,3-dinitrobenzene, and 1,4-dinitrobenzene were calculated using the B3LYP functional with 6-31G(d) basis sets. Three-dimensional energy surfaces were created, allowing each of the two C-N bonds to rotate through 64 positions. Dinitrobenzene was chosen for the study because each of the three different isomers has widely varying steric hindrances and bond hybridization, which affect the energy of each conformation of the isomers as the nitro functional groups rotate. The accuracy of the method is determined by comparison with previous theoretical and experimental results. The surfaces provide valuable insight into the mechanics of conjugated molecules. The computation of potential energy surfaces has powerful application in modeling molecular structures, making the determination of the lowest energy conformations of complex molecules far more computationally accessible.

Development of a Virtual Environment for Surface Topomorphy and Roughness Determination in Milling Operations

2008 ◽  
Vol 8 (2) ◽  
Author(s):  
Bilalis Nikolaos ◽  
Petousis Markos
Keyword(s):  
Surface Roughness ◽  
Graphical Model ◽  
Three Dimensional ◽  
Commercial Development ◽  
Machined Surface ◽  
Visualization System ◽  
Milling Operations ◽  
Machined Parts ◽  
Cloud Of Points

Surface roughness is a key parameter for determining the quality of machined parts. A graphical model for the calculation of quantitative data affecting surface roughness of machined surfaces was developed. The model allows the determination of the accurate machined surface in cloud of points form retrieved from the visualization system Z buffer in a three dimensional graphics environment developed in OPENGL. Critical quantitative parameters for surface roughness, such as RaRyRtiRz, and mean line, are determined from this topomorphy. The results together with the operations are visualized in a virtual machine shop environment developed in a commercial development toolkit.

Policy search for multi-robot coordination under uncertainty

2016 ◽  
Vol 35 (14) ◽  
pp. 1760-1778 ◽  
Author(s):  
Christopher Amato ◽  
George Konidaris ◽  
Ariel Anders ◽  
Gabriel Cruz ◽  
Jonathan P How ◽  
...  
Keyword(s):  
Search Algorithm ◽  
Infinite Horizon ◽  
Tree Representation ◽  
Policy Search ◽  
Performance Improvements ◽  
Robot Systems ◽  
Finite State ◽  
Planning Algorithm ◽  
Significant Performance ◽  
Multi Robot

We introduce a principled method for multi-robot coordination based on a general model (termed a MacDec-POMDP) of multi-robot cooperative planning in the presence of stochasticity, uncertain sensing, and communication limitations. A new MacDec-POMDP planning algorithm is presented that searches over policies represented as finite-state controllers, rather than the previous policy tree representation. Finite-state controllers can be much more concise than trees, are much easier to interpret, and can operate over an infinite horizon. The resulting policy search algorithm requires a substantially simpler simulator that models only the outcomes of executing a given set of motor controllers, not the details of the executions themselves and can solve significantly larger problems than existing MacDec-POMDP planners. We demonstrate significant performance improvements over previous methods and show that our method can be used for actual multi-robot systems through experiments on a cooperative multi-robot bartending domain.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Determination of Optimal Public Transportation Routes Using Firefly and Tabu Search Algorithms

2020 ◽  
Vol 4 (5) ◽  
pp. 884-891
Author(s):  
Salwa Salsabila Mansur ◽  
Sri Widowati ◽  
Mahmud Imrona
Keyword(s):  
Tabu Search ◽  
Public Transportation ◽  
Traffic Congestion ◽  
Search Algorithm ◽  
Urban Transportation ◽  
The Public ◽  
Comparison Results ◽  
Congestion Problems ◽  
Transportation Routes

Traffic congestion problems generally caused by the increasing use of private vehicles and public transportations. In order to overcome the situation, the optimization of public transportation’s route is required particularly the urban transportation. In this research, the performance analysis of Firefly and Tabu Search algorithm is conducted to optimize eleven public transportation’s routes in Bandung. This optimization aims to increase the dispersion of public transportation’s route by expanding the scope of route that are crossed by public transportation so that it can reach the entire Bandung city and increase the driver’s income by providing the passengers easier access to public transportations in order to get to their destinations. The optimal route is represented by the route with most roads and highest number of incomes. In this research, the comparison results between the reference route and the public transportation’s optimized route increasing the dispersion of public transportation’s route to 60,58% and increasing the driver’s income to 20,03%.

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