ОСОБЛИВОСТІ 3D МОДЕЛЮВАННЯ СТРУКТУРИ  ТРИКОТАЖУ У МАКСИМАЛЬНО РОЗТЯГНУТОМУ СТАНІ

The study aims at the development mathematical basics for software for automated construction of three-dimensional geometric models of knitwear in the most stretched state due to uniaxial stretching along the wale or course direction. Methodology. The research methods of theoretical analysis, spline theory, methods of three-dimensional geometric modeling and parameterization, computer graphics tools, programming tools were used. Findings. During the research, it was assumed that in the maximally stretched state, the tangent to the centerline of the loop at the interlacing point is located at an angle of 45º to the vertical line oriented along the wale direction. Mathematical expressions are proposed for determining the co-ordinates of the characteristic points of the loop in three-dimensional space. An algorithm and its software implementation have been developed as a separate module of the Structure 3D program, designed to create models of knitwear in a stretched state. To verify the algorithm, samples of weft knitted fabrics were made with a 8th gauge flat-bed knitting machine of para-aramid and high-molecular polyethylene threads of linear density 58.8x2 tex and 44x3 tex, respectively. The parameters of the loop structure of the samples in dry-relaxed state and under maximum uniaxial stretching along the wale and the course directions. Tensile testing of specimens was performed on the machine KaoTieh KT-7010AZ. The maximum stress state of the samples was recorded using a Micro Capture Pro microscope to further determine the changes of the loop structure parameters under the action of tensile deformation. The obtained values of the the loop structure parameters of the samples were used as input data for the construction of three-dimensional models. The deviation of the value of the length of the spline representing the centerline of the thread in the loop model from the length of the thread in the loop obtained during the analysis of the samples does not exceed 5%. Scientific novelty. An algorithm for the automated construction of 3D models of knitted structures, undergoing maximum deformations coursed by uniaxial tension along the wales or course directions, has been developed. Practical value. A separate module of the 3D Structure program has been created for the automated construction of a knitted loop undergoing maximal stretching under has been developed.

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3D Visualization for Hydrocarbon Project Design

2008 7th International Pipeline Conference, Volume 1 ◽

10.1115/ipc2008-64588 ◽

2008 ◽

Author(s):

Scott Neurauter ◽

Sabrina Szeto ◽

Matt Tindall ◽

Yan Wong ◽

Chris Wright

Keyword(s):

Spatial Data ◽

3D Visualization ◽

Dimensional Space ◽

Three Dimensional ◽

3D Models ◽

3D Analysis ◽

Cost Efficient ◽

Ground Truthing ◽

Elevation Model ◽

Visualization Techniques

3D visualization is the process of displaying spatial data to simulate and model a real three dimensional space. Using 3D visualization, Geomatic professionals are enabling pipeline engineers to make better decisions by providing an increased understanding of potential costs earlier in the design process. This paper will focus on the value of visualizing Digital Elevation Model (DEM) data through the use of hillshades and imagery-draped 3D models. From free online DEM data to high resolution Light Detection and Ranging (LiDAR) derived DEM data, the increased availability allows for a broader use of 3D visualization techniques beyond 3D analysis. Of the numerous sources available, two DEM sources will be discussed in this paper, the free low resolution DEM (CDED Level 1) and the more costly but higher resolution LiDAR based DEM. Traditional methods of evaluating potential locations for route and facilities involved a significant cost for ground truthing. Through the use of 3D visualization products, multiple potential locations can be examined for suitability without the expense of field visits for every candidate site. By focusing on the selected candidate locations using a visual desktop study, the time and expense of ground truthing all of the potential sites can be reduced significantly. Exploiting the visual value of DEM permits a productive and cost efficient methodology for initial route and facility placement on hydrocarbon projects.

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Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.704274 ◽

2021 ◽

Vol 8 ◽

Author(s):

Bhaskar Dasgupta ◽

Osamu Miyashita ◽

Takayuki Uchihashi ◽

Florence Tama

Keyword(s):

Atomic Force Microscopy ◽

Computational Modeling ◽

High Speed ◽

3D Structure ◽

Three Dimensional ◽

3D Models ◽

Computational Method ◽

Molecular Surface ◽

Force Microscopy ◽

Atomic Force

ClpB belongs to the cellular disaggretase machinery involved in rescuing misfolded or aggregated proteins during heat or other cellular shocks. The function of this protein relies on the interconversion between different conformations in its native condition. A recent high-speed-atomic-force-microscopy (HS-AFM) experiment on ClpB from Thermus thermophilus shows four predominant conformational classes, namely, open, closed, spiral, and half-spiral. Analyses of AFM images provide only partial structural information regarding the molecular surface, and thus computational modeling of three-dimensional (3D) structures of these conformations should help interpret dynamical events related to ClpB functions. In this study, we reconstruct 3D models of ClpB from HS-AFM images in different conformational classes. We have applied our recently developed computational method based on a low-resolution representation of 3D structure using a Gaussian mixture model, combined with a Monte-Carlo sampling algorithm to optimize the agreement with target AFM images. After conformational sampling, we obtained models that reflect conformational variety embedded within the AFM images. From these reconstructed 3D models, we described, in terms of relative domain arrangement, the different types of ClpB oligomeric conformations observed by HS-AFM experiments. In particular, we highlighted the slippage of the monomeric components around the seam. This study demonstrates that such details of information, necessary for annotating the different conformational states involved in the ClpB function, can be obtained by combining HS-AFM images, even with limited resolution, and computational modeling.

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Geometric modeling and development of custom libraries in the design of engineering facilities

Программные системы и вычислительные методы ◽

10.7256/2454-0714.2020.1.32292 ◽

2020 ◽

pp. 1-7

Author(s):

Elena Sergeevna Reshetnikova ◽

Irina Aleksandrovna Savelyeva ◽

Ekaterina Anatolyevna Svistunova

Keyword(s):

Design Process ◽

Computer Aided Design ◽

Geometric Modeling ◽

Three Dimensional ◽

3D Models ◽

Conveyor Belt ◽

General Idea ◽

Design Stage ◽

Preliminary Design ◽

Design Documentation

The subject of research is the process of designing a conveyor belt. The authors consider parameterization in geometric modeling of parts and components of equipment and the creation of custom libraries in Compass 3D as a means of reducing the complexity and improving the quality of the design process. The preliminary design is the design stage of the development of design documentation and aims to determine the fundamental design solutions for a general idea of the device, operating principles and dimensions of the product. It is advisable to develop a preliminary design before the stage of developing a technical project and creating design documentation. Today, at all stages of work on the project, modern computer-aided design (CAD) systems are used, which not only accelerate the design process, but also make it possible to demonstrate to the customer the finished project at the stage of making technical decisions. This allows making timely changes in accordance with the requirements of the customer and to carry out high-quality preparation of the project for its implementation. The volume and time for further stages of work depend on the timing of the presentation of the preliminary design, therefore, the use of three-dimensional modeling parametrization in CAD is an effective way for designing engineering objects. Parameterization when working with 3D models allows you to get a set of typical product designs based on a once-created model by changing the set values of the variables, which significantly reduces the time spent on the project.

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A novel 3D template for mandible and maxilla reconstruction: Rapid prototyping using stereolithography

Indian Journal of Plastic Surgery ◽

10.4103/0970-0358.173123 ◽

2015 ◽

Vol 48 (03) ◽

pp. 263-273 ◽

Cited By ~ 12

Author(s):

Samir Kumta ◽

Monica Kumta ◽

Leena Jain ◽

Shrirang Purohit ◽

Rani Ummul

Keyword(s):

Rapid Prototyping ◽

Computer Aided Design ◽

Treatment Plan ◽

3D Structure ◽

Three Dimensional ◽

Bone Grafts ◽

3D Models ◽

Mirror Image ◽

Anatomical Model ◽

Patient Counselling

ABSTRACT Introduction: Replication of the exact three-dimensional (3D) structure of the maxilla and mandible is now a priority whilst attempting reconstruction of these bones to attain a complete functional and aesthetic rehabilitation. We hereby present the process of rapid prototyping using stereolithography to produce templates for modelling bone grafts and implants for maxilla/mandible reconstructions, its applications in tumour/trauma, and outcomes for primary and secondary reconstruction. Materials and Methods: Stereolithographic template-assisted reconstruction was used on 11 patients for the reconstruction of the mandible/maxilla primarily following tumour excision and secondarily for the realignment of post-traumatic malunited fractures or deformity corrections. Data obtained from the computed tomography (CT) scans with 1-mm resolution were converted into a computer-aided design (CAD) using the CT Digital Imaging and Communications in Medicine (DICOM) data. Once a CAD model was constructed, it was converted into a stereolithographic format and then processed by the rapid prototyping technology to produce the physical anatomical model using a resin. This resin model replicates the native mandible, which can be thus used off table as a guide for modelling the bone grafts. Discussion: This conversion of two-dimensional (2D) data from CT scan into 3D models is a very precise guide to shaping the bone grafts. Further, this CAD can reconstruct the defective half of the mandible using the mirror image principle, and the normal anatomical model can be created to aid secondary reconstructions. Conclusion: This novel approach allows a precise translation of the treatment plan directly to the surgical field. It is also an important teaching tool for implant moulding and fixation, and helps in patient counselling.

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Three-Dimensional Reconstruction of Coronary Arteries and Its Application in Localization of Coronary Artery Segments Corresponding to Myocardial Segments Identified by Transthoracic Echocardiography

Computational and Mathematical Methods in Medicine ◽

10.1155/2013/783939 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Chunyan Zhong ◽

Yanli Guo ◽

Haiyun Huang ◽

Liwen Tan ◽

Yi Wu ◽

...

Keyword(s):

Coronary Arteries ◽

Transthoracic Echocardiography ◽

3D Structure ◽

Three Dimensional ◽

3D Models ◽

Localization Accuracy ◽

Significant Difference ◽

2D Ultrasound ◽

Ct Data ◽

Contrast Ct

Objectives.To establish 3D models of coronary arteries (CA) and study their application in localization of CA segments identified by Transthoracic Echocardiography (TTE).Methods.Sectional images of the heart collected from the first CVH dataset and contrast CT data were used to establish 3D models of the CA. Virtual dissection was performed on the 3D models to simulate the conventional sections of TTE. Then, we used 2D ultrasound, speckle tracking imaging (STI), and 2D ultrasound plus 3D CA models to diagnose 170 patients and compare the results to coronary angiography (CAG).Results.3D models of CA distinctly displayed both 3D structure and 2D sections of CA. This simulated TTE imaging in any plane and showed the CA segments that corresponded to 17 myocardial segments identified by TTE. The localization accuracy showed a significant difference between 2D ultrasound and 2D ultrasound plus 3D CA model in the severe stenosis group (P<0.05) and in the mild-to-moderate stenosis group (P<0.05).Conclusions.These innovative modeling techniques help clinicians identify the CA segments that correspond to myocardial segments typically shown in TTE sectional images, thereby increasing the accuracy of the TTE-based diagnosis of CHD.

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Geometrical Model of the Manufacturing Surface of the Equivalent Working Surface of the Fine Tooth Dolbyak

10.30987/graphicon-2019-1-196-200 ◽

2019 ◽

Author(s):

С. Рязанов ◽

S. Ryazanov ◽

Михаил Решетников ◽

Mihail Reshetnikov

Keyword(s):

Computer Modeling ◽

Geometric Modeling ◽

Dimensional Space ◽

Geometric Model ◽

Three Dimensional ◽

Geometrical Model ◽

Analytic Description ◽

Computer Algorithms ◽

Gear Cutting ◽

Working Surface

Existing mathematical models for calculating gearing are quite complex and do not always make it possible to quickly and accurately obtain the desired result. A simpler way to find a suitable gear option that satisfies the task is to use computer modeling and computer graphics methods, and in particular solid-state modeling algorithms. The use of geometric modeling techniques to simulate the process of shaping the working surface of gearing is based on the relative movement of intersecting objects in the form of a “workpiece-tool” system. This allows you to obtain the necessary geometric model that accurately reproduces the geometric configuration of the surfaces of the teeth of spatial gears, taking into account the technological features of their production on gear cutting machines. This information allows you to perform on the computer imitation control the movement of the cutting tool. Ultimately, this boils down to the problem of analytic description and computer representation of curves and surfaces in three-dimensional space. As the gear cutting tools, the most widely used are disk and worm modular mills (shaver), gear cutting heads, dolbyaki and lath tools. At the moment there are no computer algorithms for obtaining the “dolbyak” producing surfaces, which are obtained by a tool with a modified producing surface. A change in the geometric shape of the tool producing surface will lead to a change in its working surfaces, which may lead to an improvement in their contact. This article shows the application of the developed methods and algorithms of geometric and computer modeling, which are intended for shaping the working surfaces of the Dolbyak tool. Their application will speed up the process of calculating intermediate adjustments of machines used for cutting gears, bypassing complex mathematical calculations that, under conditions of aging of the gear-cutting machines, their wear and the inevitable reduction in the accuracy of their kinematic chains.

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REALDIST: Real-valued protein distance prediction

10.1101/2020.11.28.402214 ◽

2020 ◽

Cited By ~ 1

Author(s):

Badri Adhikari

Keyword(s):

Structure Prediction ◽

3D Structure ◽

Three Dimensional ◽

Prediction Method ◽

3D Models ◽

Classification Problem ◽

Intermediate Step ◽

Protein Distance ◽

Multi Class Classification ◽

Distance Prediction

AbstractProtein structure prediction continues to stand as an unsolved problem in bioinformatics and biomedicine. Deep learning algorithms and the availability of metagenomic sequences have led to the development of new approaches to predict inter-residue distances—the key intermediate step. Different from the recently successful methods which frame the problem as a multi-class classification problem, this article introduces a real-valued distance prediction method REALDIST. Using a representative set of 43 thousand protein chains, a variant of deep ResNet is trained to predict real-valued distance maps. The contacts derived from the real-valued distance maps predicted by this method, on the most difficult CASP13 free-modeling protein datasets, demonstrate a long-range top-L precision of 52%, which is 17% higher than the top CASP13 predictor Raptor-X and slightly higher than the more recent trRosetta method. Similar improvements are observed on the CAMEO ‘hard’ and ‘very hard’ datasets. Three-dimensional (3D) structure prediction guided by real-valued distances reveals that for short proteins the mean accuracy of the 3D models is slightly higher than the top human predictor AlphaFold and server predictor Quark in the CASP13 competition.

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The 3D architecture of the pepper (Capsicum annum) genome and its relationship to function and evolution

10.1101/2021.12.10.470457 ◽

2021 ◽

Author(s):

Yi Liao ◽

Juntao Wang ◽

Zhangsheng Zhu ◽

Yuanlong Liu ◽

Jinfeng Chen ◽

...

Keyword(s):

Gene Expression ◽

Dimensional Space ◽

3D Structure ◽

Three Dimensional ◽

Structural Evolution ◽

Integrated Analysis ◽

Gene Clustering ◽

Plant Genomes ◽

3D Genome ◽

Contact Maps

AbstractThe architecture of topologically associating domains (TADs) varies across plant genomes. Understanding the functional consequences of this diversity requires insights into the pattern, structure, and function of TADs. Here, we present a comprehensive investigation of the 3D genome organization of pepper (Capsicum annuum) and its association with gene expression and genomic variants. We report the first chromosome-scale long-read genome assembly of pepper and generate Hi-C contact maps for four tissues. The contact maps indicate that 3D structure varies somewhat across tissues, but generally the genome was segregated into subcompartments that were correlated with transcriptional state. In addition, chromosomes were almost continuously spanned by TADs, with the most prominent found in large genomic regions that were rich in retrotransposons. A substantial fraction of TAD boundaries were demarcated by chromatin loops, suggesting loop extrusion is a major mechanism for TAD formation; many of these loops were bordered by genes, especially in highly repetitive regions, resulting in gene clustering in three dimensional space. Integrated analysis of Hi-C profiles and transcriptomes showed that change in 3D chromatin structures (e.g. subcompartments, TADs, and loops) was not the primary mechanism contributing to differential gene expression between tissues, but chromatin structure does play a role in transcription stability. TAD boundaries were significantly enriched for breaks of synteny and depletion of sequence variation, suggesting that TADs constrain patterns of genome structural evolution in plants. Together, our work provides insights into principles of 3D genome folding in large plant genomes and its association with function and evolution.

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Identification and “in silico” Structural Analysis of the Glutamine-rich Protein Qrp (YheA) in Staphylococcus Aureus

The Open Bioinformatics Journal ◽

10.2174/1875036201912010018 ◽

2019 ◽

Vol 12 (1) ◽

pp. 18-29

Author(s):

Javier Escobar-Perez ◽

Katterine Ospina-Garcia ◽

Zayda Lorena Corredor Rozo ◽

Ricaurte Alejandro Marquez-Ortiz ◽

Jaime E Castellanos ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Structural Analysis ◽

Protein Function ◽

In Silico ◽

3D Structure ◽

Three Dimensional ◽

3D Models ◽

Protein Domain ◽

Dimensional Structure ◽

Biofilm Growth

Background: YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established. Objective: In this study, we identified and performed an “in silico” structural analysis of the YheA protein, another com_ylbF-containing protein, in the opportunistic pathogen Staphylococcus aureus. Methods: The search of the yheA gene was performed using BLAST-P and tBLASn algorithms. The three-dimensional (3D) models of YheA, as well as YlbF and YmcA proteins, were built using the I-TASSER and Quark programs. The identification of the native YheA in Staphylococcus aureus was carried out through chromatography using the FPLC system. Results: We found that YheA protein is more widely distributed in Gram-positive bacteria than YlbF and YmcA. Two new and important characteristics for YheA and other com_ylbF-containing proteins were found: a highly conserved 3D structure and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. Additionally, we established that Staphylococcus aureus expresses YheA protein in both planktonic growth and biofilm. Finally, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus. Conclusion: The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates. Finally, Staphylococcus aureus expresses the Grp (YheA) protein in both planktonic and biofilm growth.

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Algorithmic Complex for Solving of Problems with Quadrics Using Imaginary Geometric Images

Geometry & Graphics ◽

10.12737/2308-4898-2020-3-32 ◽

2020 ◽

Vol 8 (2) ◽

pp. 3-32

Author(s):

Denis Voloshinov

Keyword(s):

Geometric Modeling ◽

Dimensional Space ◽

Three Dimensional ◽

Conjugate Points ◽

Complex Conjugate ◽

Real Point ◽

Projection Model ◽

Arbitrary Plane ◽

Intersection Line ◽

Three Dimensional Space

The paper is devoted to the consideration of a number of issues related to the creation of an algorithmic complex designed to solve positional and metric problems with quadrics on a projection model . A feature of the complex is the active use of geometric schemes and algorithms involving imaginary geometric images. In the paper has been presented a detailed description of constructive geometric algorithms for constructing of conics, quadrics and associated geometric images in a system of constructive geometric modeling – Simplex. All the discussed algorithms are available for independent repetition by the reader. In the paper have been presented and implemented algorithms for constructing conic from a point, a polar, and three points; constructing conic from two pairs of complex conjugate points and one real point; determination of a point on a quadric’s surface; setting a quadric by nine points in three-dimensional space. A new alternative frame of the quadric has been considered, based on which have been solved problems of constructing a tangent and a normal to the quadric, finding an intersection line of an arbitrary plane with the quadric, and performing polar and inverse transformations with respect to the quadric. Have been proposed algorithms for constructing an autopolar tetrahedron with respect to the quadric, and for constructing a conic from an autopolar triangle and two points. Have been considered problems of determining a collinear transformation in three-dimensional space and control the quadric through it. The implementation of the algorithms considered in the paper allowed conclude that there is an urgent need to develop tools for modeling imaginary conics, without which the complex of solving problems with quadrics cannot be taken for the complete one.

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