scholarly journals Modeling and Visualization of Rice Root Based on Morphological Parameters

2019 ◽  
Author(s):  
Le Yang ◽  
Peng Shao
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Morphological Structure ◽  
Growth Function ◽  
Growth Characteristics ◽  
Rice Root ◽  
Morphological Parameters ◽  
Rice Roots ◽  
Spline Curves ◽  
Growth Change

AbstractTo clarify the morphological distributional characteristic of rice roots, the “root box” experiments are conducted to extract various morphological parameters of roots. On the basis of experiments, in this paper, the rice root model based on morphological parameters is constructed with B-spline curves by analyzing the topological structure of rice roots, quantifying their biological characteristics, summarizing the morphological structure and growth characteristics and improving the Cubic growth function to describe the growth change of rice roots. Meanwhile, the output accuracy of the model is tested. Finally, the dynamic simulation of rice root growth characteristics in three-dimensional space is implemented by using Visual C++ and OpenGL standard graphics library. The compared results demonstrate that the model could faithfully simulate the dynamic growing process of rice roots, and help to enrich the methods of digitization and visualization for roots of other crops.

Research on the Construction and Visualization of a Three-Dimensional Model of Rice Root Growth

2020 ◽  
Vol 36 (6) ◽  
pp. 847-857
Author(s):  
Le   Yang ◽  
Panpan   Wu ◽  
Suyong   Yang ◽  
Peng   Shao
Keyword(s):  
Root Growth ◽  
Growth Model ◽  
Three Dimensional ◽  
Morphological Characteristics ◽  
Rice Root ◽  
Model Output ◽  
Rice Roots ◽  
L System ◽  
Growth Laws ◽  
Dynamic Growth

HighlightsThis article proposes a three-dimensional rice root growth model based on the differential L-system.We tested the accuracy of the model output, and the measured values and the simulated values were compared.A three-dimensional visualization of the growth simulation system was implemented, and the dynamic growth process of rice roots was visually reproduced.Abstract. Three-dimensional visualization studies on the morphological characteristics of rice root systems are important for improving farmland management and for the selective breeding and genetic improvement of rice. To clarify the rules governing the structure and distribution of rice roots, the three-dimensional (3D) coordinates and morphological parameters of rice roots were measured in hydroponic experiments at different growing periods, and the rice root structure was measured with a high degree of accuracy. The initial position, growth direction, and rate were then determined via statistical analysis of the data. In this article, a 3D rice root growth model based on the differential L-system is proposed; in this system, the biological characteristics based on the topological structure and the actual growth laws of rice roots are quantified. We adopted the growing degree day (GDD) as the driving factor that describes the growth law of rice roots and tested the accuracy of the model output. In this model, a 3D visualization of the growth simulation system of rice roots is implemented via Visual C++ and the OpenGL standard library on the basis of algorithms for the constructed 3D rice root growth model. The model output realistically recreates the dynamic growth process of rice roots under different conditions. A large amount of experimental data and comparative analysis show that the average accuracies achieved by the proposed system concerning total root length, root surface area and root volume are 96.95%, 95.97%, and 93.98%, respectively. These results verify the high reliability of the constructed model and the effective simulation of the morphological characteristics and growth laws of rice roots at different growth periods, laying the foundation for future research on the laws of changes in morphological structure and the physiological and ecological factors of rice roots at different growth stages. Keywords: Differential L-system, Rice roots, Simulation, Three-dimensional growth model, Visualization.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

Diffraction contrast of dislocations in icosahedral quasicrystals

1990 ◽  
Vol 48 (4) ◽  
pp. 454-455
Author(s):  
K. Urban ◽  
Z. Zhang ◽  
M. Wollgarten ◽  
D. Gratias
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Complete Characterization ◽  
Extinction Condition ◽  
Burgers Vector ◽  
Diffraction Contrast ◽  
Lattice Geometry ◽  
Reference Space ◽  
Icosahedral Quasicrystals ◽  
The One

Recently dislocations have been observed by electron microscopy in the icosahedral quasicrystalline (IQ) phase of Al65Cu20Fe15. These dislocations exhibit diffraction contrast similar to that known for dislocations in conventional crystals. The contrast becomes extinct for certain diffraction vectors g. In the following the basis of electron diffraction contrast of dislocations in the IQ phase is described. Taking account of the six-dimensional nature of the Burgers vector a “strong” and a “weak” extinction condition are found.Dislocations in quasicrystals canot be described on the basis of simple shear or insertion of a lattice plane only. In order to achieve a complete characterization of these dislocations it is advantageous to make use of the one to one correspondence of the lattice geometry in our three-dimensional space (R3) and that in the six-dimensional reference space (R6) where full periodicity is recovered . Therefore the contrast extinction condition has to be written as gpbp + gobo = 0 (1). The diffraction vector g and the Burgers vector b decompose into two vectors gp, bp and go, bo in, respectively, the physical and the orthogonal three-dimensional sub-spaces of R6.

Flavin radicals, conformational sampling and robust design principles in interprotein electron transfer: the trimethylamine dehydrogenase-electron-transferring flavoprotein complex

2004 ◽  
Vol 71 ◽  
pp. 1-14
Author(s):  
David Leys ◽  
Jaswir Basran ◽  
François Talfournier ◽  
Kamaldeep K. Chohan ◽  
Andrew W. Munro ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Kinetic Studies ◽  
Molecular Assembly ◽  
Conformational Sampling ◽  
Trimethylamine Dehydrogenase ◽  
Key Residues ◽  
Electron Transferring Flavoprotein ◽  
Electron Transfer Complex

TMADH (trimethylamine dehydrogenase) is a complex iron-sulphur flavoprotein that forms a soluble electron-transfer complex with ETF (electron-transferring flavoprotein). The mechanism of electron transfer between TMADH and ETF has been studied using stopped-flow kinetic and mutagenesis methods, and more recently by X-ray crystallography. Potentiometric methods have also been used to identify key residues involved in the stabilization of the flavin radical semiquinone species in ETF. These studies have demonstrated a key role for 'conformational sampling' in the electron-transfer complex, facilitated by two-site contact of ETF with TMADH. Exploration of three-dimensional space in the complex allows the FAD of ETF to find conformations compatible with enhanced electronic coupling with the 4Fe-4S centre of TMADH. This mechanism of electron transfer provides for a more robust and accessible design principle for interprotein electron transfer compared with simpler models that invoke the collision of redox partners followed by electron transfer. The structure of the TMADH-ETF complex confirms the role of key residues in electron transfer and molecular assembly, originally suggested from detailed kinetic studies in wild-type and mutant complexes, and from molecular modelling.

Topics in Quaternion Linear Algebra

2014 ◽  
Author(s):  
Leiba Rodman
Keyword(s):  
Linear Algebra ◽  
Complex Analysis ◽  
Dimensional Space ◽  
Applied Mathematics ◽  
Three Dimensional ◽  
Number System ◽  
Graduate Course ◽  
Open Problems ◽  
Unpublished Research ◽  
Reference Tool

Quaternions are a number system that has become increasingly useful for representing the rotations of objects in three-dimensional space and has important applications in theoretical and applied mathematics, physics, computer science, and engineering. This is the first book to provide a systematic, accessible, and self-contained exposition of quaternion linear algebra. It features previously unpublished research results with complete proofs and many open problems at various levels, as well as more than 200 exercises to facilitate use by students and instructors. Applications presented in the book include numerical ranges, invariant semidefinite subspaces, differential equations with symmetries, and matrix equations. Designed for researchers and students across a variety of disciplines, the book can be read by anyone with a background in linear algebra, rudimentary complex analysis, and some multivariable calculus. Instructors will find it useful as a complementary text for undergraduate linear algebra courses or as a basis for a graduate course in linear algebra. The open problems can serve as research projects for undergraduates, topics for graduate students, or problems to be tackled by professional research mathematicians. The book is also an invaluable reference tool for researchers in fields where techniques based on quaternion analysis are used.

Extension of the Spatial PDI Model to Three Dimensions

1997 ◽  
Vol 84 (1) ◽  
pp. 176-178
Author(s):  
Frank O'Brien
Keyword(s):  
Population Density ◽  
Dimensional Space ◽  
Finite Lattice ◽  
Three Dimensional ◽  
Upper Bounds ◽  
Three Dimensions ◽  
Lower And Upper Bounds ◽  
Density Index ◽  
Three Dimensional Space

The author's population density index ( PDI) model is extended to three-dimensional distributions. A derived formula is presented that allows for the calculation of the lower and upper bounds of density in three-dimensional space for any finite lattice.

A Peptoid with Extended Shape in Water

2019 ◽  
Author(s):  
Jumpei Morimoto ◽  
Yasuhiro Fukuda ◽  
Takumu Watanabe ◽  
Daisuke Kuroda ◽  
Kouhei Tsumoto ◽  
...  
Keyword(s):  
Spectroscopic Analysis ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Biomolecular Recognition ◽  
Biological Application ◽  
New Class ◽  
Proteolytic Resistance ◽  
Pharmacokinetic Properties ◽  
Optically Pure ◽  
Three Dimensional Space

<div> <div> <div> <p>“Peptoids” was proposed, over decades ago, as a term describing analogs of peptides that exhibit better physicochemical and pharmacokinetic properties than peptides. Oligo-(N-substituted glycines) (oligo-NSG) was previously proposed as a peptoid due to its high proteolytic resistance and membrane permeability. However, oligo-NSG is conformationally flexible and is difficult to achieve a defined shape in water. This conformational flexibility is severely limiting biological application of oligo-NSG. Here, we propose oligo-(N-substituted alanines) (oligo-NSA) as a new peptoid that forms a defined shape in water. A synthetic method established in this study enabled the first isolation and conformational study of optically pure oligo-NSA. Computational simulations, crystallographic studies and spectroscopic analysis demonstrated the well-defined extended shape of oligo-NSA realized by backbone steric effects. The new class of peptoid achieves the constrained conformation without any assistance of N-substituents and serves as an ideal scaffold for displaying functional groups in well-defined three-dimensional space, which leads to effective biomolecular recognition. </p> </div> </div> </div>

Sign in / Sign up

Export Citation Format

Share Document