scholarly journals 3D Perception of Maximum Density Zone on Ramachandran Plots for Zika Virus Protein Structures

2016 ◽  
Author(s):  
Mayukh Mukhopadhyay ◽  
Parama Bhaumik
Keyword(s):  
Zika Virus ◽  
Rapid Development ◽  
Protein Structures ◽  
Three Dimensional ◽  
Small Region ◽  
Virus Protein ◽  
Two Dimensional ◽  
True Nature ◽  
Data Points ◽  
Ramachandran Plots

AbstractThe Ramachandran plot is among the most central concepts in structural biology which uses torsion angles to describe polypeptide and protein conformation. To help visualize the features of high-fidelity Ramachandran plots, it is helpful to look beyond the common two-dimensional psi-phi-plot, which for a large dataset does not serve very well to convey the true nature of the distribution. In particular, when a large subset of the observations is found very narrowly distributed within one small region, this is not well seen in the simple plot because the data points congest one another. Zika Virus (ZIKV) protein databank has been chosen as specimen for analysis. This is because the structure, tropism, and pathogenesis of ZIKV are largely unknown and are the focus of current investigations in an effort to address the need for rapid development of vaccines and therapeutics. After a brief survey on Zika Virus, it is shown that when a dense dataset of ZIKV protein databank is passed through a colour-coded scaled algorithm, a three dimensional plot gets generated which gives a much more compelling impression of the proportions of residues in the different parts of the protein rather than representing it in a normal two dimensional psi-phi plot.

Design of a Two-Piece Brassiere Cup From its Data Points Toward its Automation

2020 ◽  
Author(s):  
Kotaro Yoshida ◽  
Hidefumi Wakamatsu ◽  
Eiji Morinaga ◽  
Takahiro Kubo
Keyword(s):  
Three Dimensional ◽  
Developable Surface ◽  
Two Dimensional ◽  
Trial And Error ◽  
Design Efficiency ◽  
Developable Surfaces ◽  
Data Points ◽  
Dimensional Shape ◽  
The Given ◽  
Three Dimensional Shape

Abstract A method to design the two-dimensional shapes of patterns of two piece brassiere cup is proposed when its target three-dimensional shape is given as a cloud of its data points. A brassiere cup consists of several patterns and their shapes are designed by repeatedly making a paper cup model and checking its three-dimensional shape. For improvement of design efficiency of brassieres, such trial and error must be reduced. As a cup model for check is made of paper not cloth, it is assumed that the surface of the model is composed of several developable surfaces. When two lines that consist in the developable surface are given, the surface can be determined. Then, the two-piece brassiere cup can be designed by minimizing the error between the surface and given data points. It was mathematically verified that the developable surface calculated by our propose method can reproduce the given data points which is developable surface.

Algorithm of Hardy Function Interpolation and its Visualization in the Formation of the Virtual Battlefield Terrain

2013 ◽  
Vol 709 ◽  
pp. 495-498
Author(s):  
Shi Bin Liu ◽  
Cheng Wang ◽  
Yan Ping Yang ◽  
Xing Yan Liu
Keyword(s):  
Three Dimensional ◽  
Reference Value ◽  
Two Dimensional ◽  
C Language ◽  
Hardy Function ◽  
Data Points ◽  
Comparison And Analysis ◽  
Searching Method ◽  
Dimensional Surface

this thesis puts forward the idea of using the searching method to retrieve two kinds of data points of the circle and the square to generate DEM data of the collected discrete points by means of using C# language and OpenGL DLL, thus realizing the visualization of the three-dimensional virtual terrain from contours on the two-dimensional surface. This thesis makes a comparison and analysis of the visualization effect which indicates that this algorithm is quick and effective. This research has a certain reference value for the formation of the virtual battlefield terrain.

scholarly journals A Study of Modified Infotaxis Algorithms in 2D and 3D Turbulent Environments

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Shurui Fan ◽  
Dongxia Hao ◽  
Xudong Sun ◽  
Yusuf Mohamed Sultan ◽  
Zirui Li ◽  
...  
Keyword(s):  
Rapid Development ◽  
Three Dimensional ◽  
Evaluation Criteria ◽  
Research Field ◽  
Sensor Data ◽  
Sensor Technology ◽  
Two Dimensional ◽  
Reward Function ◽  
Autonomous Search ◽  
Hazardous Gas

Emergency response to hazardous gases in the environment is an important research field in environmental monitoring. In recent years, with the rapid development of sensor technology and mobile device technology, more autonomous search algorithms for hazardous gas emission sources are proposed in uncertain environment, which can avoid emergency personnel from contacting hazardous gas in a short distance. Infotaxis is an autonomous search strategy without a concentration gradient, which uses scattered sensor data to track the location of the release source in turbulent environment. This paper optimizes the imbalance of exploitation and exploration in the reward function of Infotaxis algorithm and proposes a mobile strategy for the three-dimensional scene. In two-dimensional and three-dimensional scenes, the average steps of search tasks are used as the evaluation criteria to analyze the information trend algorithm combined with different reward functions and mobile strategies. The results show that the balance between the exploitation item and exploration item of the reward function proposed in this paper is better than that of the reward function in the Infotaxis algorithm, no matter in the two-dimensional scenes or in the three-dimensional scenes.

Centrifugal instability of an oscillatory flow over periodic ripples

1990 ◽  
Vol 217 ◽  
pp. 1-32 ◽  
Author(s):  
Tetsu Hara ◽  
Chiang C. Mei
Keyword(s):  
Oscillatory Flow ◽  
Sandy Beach ◽  
Three Dimensional ◽  
Small Region ◽  
Oscillating Flow ◽  
Two Dimensional ◽  
Steady Streaming ◽  
Centrifugal Instability ◽  
Two Dimensional Flow ◽  
Finite Slope

An oscillating flow over a sandy beach can initiate and enhance the formation of bed ripples, with crests perpendicular to the direction of the ambient oscillation. Under certain circumstances, bridges may develop to span adjacent ripple crests, resulting in a brick pattern. It has been suggested that the onset of this transition is due to a three-dimensional centrifugal instability of an otherwise two-dimensional flow over periodic long-crested ripples. Here we analyse theoretically such an instability by assuming that the ripples are rigid and smooth. Two complementary cases are studied. We first consider a weak ambient oscillation over ripples of finite slope in Case (i). The three-dimensional disturbance is found to be localized in a small region either along the crests or along the troughs. In Case (ii) we analyse finite oscillations over ripples of mild slope. The region influenced by the instability is now comparable with a ripple wavelength and the unstable disturbance along adjacent ripples may interact with each other. Four types of harmonic and subharmonic instabilities are found. The associated steady streaming close to the ripple surface shows various tendencies of possible sand accumulations, some of which appear to be qualitatively relevant to the initiation of brick-patterned ripples.

Application on the Virtual Campus Making with 3D Max and VRP Technology

2013 ◽  
Vol 753-755 ◽  
pp. 1295-1298
Author(s):  
Hui Ying Zhao ◽  
Li Bo Qiu ◽  
You Ming Liu ◽  
Qi Feng ◽  
Zhi Yong Huang ◽  
...  
Keyword(s):  
Virtual Reality ◽  
Rapid Development ◽  
Three Dimensional ◽  
Computer Software ◽  
Two Dimensional ◽  
Virtual Reality Technology ◽  
Virtual Campus ◽  
Campus Environment ◽  
Angle Rotation ◽  
Software And Hardware

With the rapid development of computer software and hardware technology, 3D technology and virtual reality technology is acquiring a greater growing space. Three-dimensional virtual campus environment compared with the traditional two-dimensional campus graphics more intuitive, vivid, true-to-life. More convenient to operate, you can choose a different camera pan any, the viewpoint conversion, angle rotation.

scholarly journals Two- and three-dimensional wake transitions of an impulsively started uniformly rolling circular cylinder

2017 ◽  
Vol 826 ◽  
pp. 32-59 ◽  
Author(s):  
F. Y. Houdroge ◽  
T. Leweke ◽  
K. Hourigan ◽  
M. C. Thompson
Keyword(s):  
Stability Analysis ◽  
Circular Cylinder ◽  
Rapid Development ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensional ◽  
Dimensional Flow ◽  
Instability Modes ◽  
Two Dimensional Flow ◽  
Lift And Drag

This paper presents the characteristics of the different stages in the evolution of the wake of a circular cylinder rolling without slipping along a wall at constant speed, acquired through numerical stability analysis and two- and three-dimensional numerical simulations. Reynolds numbers between 30 and 300 are considered. Of importance in this study is the transition to three-dimensionality from the underlying two-dimensional periodic flow and, in particular, the way that the associated transitions influence the fluid forces exerted on the cylinder and the development and the structure of the wake. It is found that the steady two-dimensional flow becomes unstable to three-dimensional perturbations at $Re_{c,3D}=37$, and that the transition to unsteady two-dimensional flow – or periodic vortex shedding – occurs at $Re_{c,2D}=88$, thus validating and refining the results of Stewart et al. (J. Fluid Mech. vol. 648, 2010, pp. 225–256). The main focus here is on Reynolds numbers beyond the transition to unsteady flow at $Re_{c,2D}=88$. From impulsive start up, the wake almost immediately undergoes transition to a periodic two-dimensional wake state, which, in turn, is three-dimensionally unstable. Thus, the previous three-dimensional stability analysis based on the two-dimensional steady flow provides only an element of the full story. Floquet analysis based on the periodic two-dimensional flow was undertaken and new three-dimensional instability modes were revealed. The results suggest that an impulsively started cylinder rolling along a surface at constant velocity for $Re\gtrsim 90$ will result in the rapid development of a periodic two-dimensional wake that will be maintained for a considerable time prior to the wake undergoing three-dimensional transition. Of interest, the mean lift and drag coefficients obtained from full three-dimensional simulations match predictions from two-dimensional simulations to within a few per cent.

scholarly journals Using a multiple variogram approach to improve the accuracy of subsurface geological models

2018 ◽  
Vol 55 (7) ◽  
pp. 786-801 ◽  
Author(s):  
Kelsey MacCormack ◽  
Emmanuelle Arnaud ◽  
Beth L. Parker
Keyword(s):  
Groundwater Resources ◽  
Rapid Development ◽  
Regional Scale ◽  
Three Dimensional ◽  
Regional Model ◽  
Field Development ◽  
Model Domain ◽  
Geological Models ◽  
Source Water Protection ◽  
Data Points

Subsurface geological models are often used to visualize and analyze the nature, geometry, and variability of geologic and hydrogeologic units in the context of groundwater resource studies. The development of three-dimensional (3D) subsurface geological models covering increasingly larger model domains has steadily increased in recent years, in step with the rapid development of computing technology and software, and the increasing need to understand and manage groundwater resources at the regional scale. The models are then used by decision makers to guide activities and policies related to source water protection, well field development, and industrial or agricultural water use. It is important to ensure that the modelling techniques and procedures are able to accurately delineate and characterize the heterogeneity of the various geological environments included within the regional model domain. The purpose of this study is to examine if 3D stratigraphic models covering complex Quaternary deposits can be improved by splitting the regional model into multiple submodels based on the degree of variability observed between surrounding data points and informed by expert geological knowledge of the geological–depositional framework. This is demonstrated using subsurface data from the Paris Moraine area near Guelph in southern Ontario. The variogram models produced for each submodel region were able to better characterize the data variability, resulting in a more geologically realistic interpolation of the entire model domain as demonstrated by the comparison of the model output with preexisting maps of surficial geology and bedrock topography as well as depositional models for these complex glacial environments. Importantly, comparison between model outputs reveals significant differences in the resulting subsurface stratigraphy, complexity, and variability, which would in turn impact groundwater flow model predictions.

Cryo-EM and Single Particles

Physiology ◽  
2006 ◽  
Vol 21 (1) ◽  
pp. 13-18 ◽  
Author(s):  
Liguo Wang ◽  
Fred J. Sigworth
Keyword(s):  
Electron Microscope ◽  
Membrane Protein ◽  
Single Particle ◽  
Protein Structures ◽  
Three Dimensional ◽  
Computer Processing ◽  
Two Dimensional ◽  
Single Particles ◽  
Macromolecular Assemblies ◽  
Particle Images

Cryoelectronmicroscopy is a method for the imaging of macromolecules in the electron microscope. It was originally developed to determine membrane protein structures from two-dimensional crystals, but more recently “single-particle” techniques have become powerful and popular. Three-dimensional reconstructions are obtained from sets of single-particle images by extensive computer processing; the methods are being applied to many macromolecular assemblies.

Assessing Circularity in Three Dimensions1

2000 ◽  
Vol 123 (1) ◽  
pp. 128-134 ◽  
Author(s):  
Shuo-Yan Chou ◽  
Shih-Wei Lin ◽  
Chien-Hong Chen
Keyword(s):  
Cross Section ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Coordinate Measuring Machines ◽  
Single Plane ◽  
Research Designs ◽  
Data Points ◽  
Three Dimensional Space ◽  
Assessment Results

This research resolves an inconsistency problem that arises from assessing circularity of workpiece measured by coordinate measuring machines (CMMs). Although the notion of circularity is employed to constrain two-dimensional circular features, in practice the measured points are obtained in a three-dimensional space and are in general not in the same plane, let alone being in a “perpendicular” cross-section. All of the algorithms currently used for assessing circularity deal with data in a single plane that is perpendicular to the axis of a cylindrical feature from which the circular feature is extracted. This discrepancy causes the assessed circularity significantly departing from the actual circularity and resulting in rejection of in-tolerance parts. This research designs a compensation procedure for deriving two-dimensional data from three-dimensional biased measured points. The circularity is assessed based on the compensated two-dimensional data points. The assessment results with the compensation are compared with those without compensation. A program containing a variety of implementations of form fitting algorithms is developed and used to illustrate the improvement on the accuracy of assessment.

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