• Title/Summary/Keyword: Three-Dimensional Modelling

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Computer-Aided Drug Discovery in Plant Pathology

  • Shanmugam, Gnanendra;Jeon, Junhyun
    • The Plant Pathology Journal
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    • v.33 no.6
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    • pp.529-542
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    • 2017
  • Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.

Ocean Outfall Modelling with the Particle Tracking Method (입자추적법을 이용한 해양방류구 모델링)

  • Jung, Yun-Chul
    • Journal of Navigation and Port Research
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    • v.26 no.5
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    • pp.563-569
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    • 2002
  • To overcome the weaknesses of conventional finite difference model in pollutant dispersion modelling, the particle tracking method is used. In this study, a three dimensional particle tracking model which can be used in Princeton Ocean Model was developed and verified through the various numerical tests. Usability of the model was also confirmed through the ocean outfall modelling in Tampa Bay, Florida. As it is expected, random walk model showed the less dispersion in a range compared to the conventional finite difference model and its reason is estimated due to an error from numerical diffusion which the conventional model holds. This newly developed model is expected to be used in various ocean dispersion modelling.

Decision of Optimal Density of Airbone LiDAR Points for City zone (도시지역을 위한 항공라이다의 최적 점 밀도 결정)

  • Kim, Kam-Lae;Kim, Sang-Bong;Kim, Nam-Yong
    • Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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    • v.27 no.4
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    • pp.445-452
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    • 2009
  • Through the Airbone LiDAR point, the study for three-dimensional modeling of the city zone has been in progress. So, deciding the Density of Airbone LiDAR point for that is very important to get a result of three-dimensional modeling of the city zone and make efficient use of airbone LiDAR. This study made the standard density to decide the optimum density of Airbone LiDAR point in the city zone. Through each standard density point of DSM and the outline of the buildings, It executed the visual evaluation and the accuracy inspection to decide the optimum density point, and presented the optimum density for the airbone LiDAR point in the city zone.

Three-dimensional modelling of water flow due to leakage from pressurized buried pipe

  • Zhu, Hong;Zhang, Limin;Chen, Chen;Chan, Kit
    • Geomechanics and Engineering
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    • v.16 no.4
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    • pp.423-433
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    • 2018
  • A three-dimensional model is constructed to simulate water infiltration in an unsaturated slope from a leaking pipe. Adaptive mesh refinement and time stepping are used, assisted by an automatic procedure for progressive steepening of the hydraulic property function for better convergence. The model is justified by comparing the simulated results with experimental data. Steady-state flow is investigated considering various pipe water pressures, locations and sizes of the opening, and soil layering. The opening size significantly affects the soaked zone around the pipe. Preferential flow dominates along the pipe longitudinal direction in the presence of a loose backfill around the pipe.

Prediction of Urban Development and Cityscape with a Simulation Model (시뮬레이션 모형을 이용한 도시 개발형태 및 경관의 변화 예측)

  • 이인성;김충식
    • Journal of the Korean Institute of Landscape Architecture
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    • v.32 no.3
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    • pp.106-113
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    • 2004
  • The shapes(mass) of buildings are determined by many interrelated factors, such as planning and building regulations, the size and shape of building parcels, and adjoining road conditions. Understanding the effects of the determinants on the building shapes is not a simple task because of the multiplicity and complex interrelationships of the determinants. This study developed a prototype of three dimensional computer model that can simulates the determination process of building shape using GIS and CAD techniques. A commercial block in the south of Seoul was selected for the case study. Several methods of building height control were applied, and their effects on the cityscape were evaluated. The results shows that the three dimensional computer modelling offers an effective means for evaluating the effects of planning and building regulations. The implication of the case study and future research directions were discussed.

A Hydroelastic Response Analysis of a Very Large Floating Structure of Barge-Type in Waves (바아지식 초대형 부유 구조물의 유탄성 응답 해석)

  • Gu, Ja-Sam;Jo, Hyo-Je;Kim, Byeong-Hyeon;Lee, Chang-Ho
    • Journal of Ocean Engineering and Technology
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    • v.12 no.2 s.28
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    • pp.43-56
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    • 1998
  • A barge-type structure has been recently watched since The Floating Structures Association of Japan proposed the new concept as the most suitable one of floating airports. In this paper, the method, which is based on a combination of a three-dimensional source distribution method and the wave interaction theory is applied to very large floating structure of barge-type. The calculated results show good agreement with the experimental and calculated ones by Yago and remarkable characteristics concerning the hydroelastic behavior of the very large floating structure on the effects of hydrodynamic interactions and choice of body modelling.

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A Study on the Dynamics Modeling of Hydrostatic tables (유정압안내면의 동적 Modeling에 관한 연구)

  • 노승국;이찬흥;박천홍
    • Proceedings of the Korean Society of Precision Engineering Conference
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    • 1996.11a
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    • pp.643-647
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    • 1996
  • The dynamic behavior of hydrostatic table is represented as the theoretical model, 1-dof, 2-dof rigid body spring-damper system, and finite element model. By the experimental and theoretical methods, the validity of these models and some other dynamic behaviors, such as the effects of unbalanced load and three dimensional motion, are investigated. To make easier to consider the dynamic behavior of hydrostatic table in design process, the stiffness and damping coefficients are calculated using the simple approximation method delived from the mass flow continuity condition, and compared with experimental results.

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Three-Dimensional Modelling and Sensitivity Analysis for the Stability Assessment of Deep Underground Repository

  • Kwon, S.;Park, J.H.;Park, J.W.;Kang, C.H.
    • Nuclear Engineering and Technology
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    • v.33 no.6
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    • pp.605-618
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    • 2001
  • For the mechanical stability assessment of a deep underground high-level waste repository. computer simulations using FLAC3D were carried out and important parameters including stress ratio, depth, tunnel size, joint spacing, and joint properties were chosen from sensitivity analysis. The main effect as well as the interaction effect between the important parameters could be investigated effectively using fractional factorial design . In order to analyze the stability of the disposal tunnel and deposition hole in a discontinuous rock mass, different modelings were performed under different conditions using 3DEC and the influence of joint distribution and properties, rock properties and stress ratio could be determined. From the three dimensional modelings, it was concluded that the conceptual repository design was mechanically stable even in a discontinuous rock mass.

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A radial point interpolation method for 1D contaminant transport modelling through landfill liners

  • Praveen Kumar, R.;Dodagoudar, G.R.
    • Geomechanics and Engineering
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    • v.2 no.2
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    • pp.141-156
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    • 2010
  • In the framework of meshfree methods, a new methodology is developed based on radial point interpolation method (RPIM). This methodology is applied to a one-dimensional contaminant transport modelling in the saturated porous media. The one-dimensional form of advection-dispersion equation involving reactive contaminant is considered in the analysis. The Galerkin weak form of the governing equation is formulated using 1D meshfree shape functions constructed using thin plate spline radial basis functions. MATLAB code is developed to obtain the numerical solution. Numerical examples representing various phenomena, which occur during migration of contaminants, are presented to illustrate the applicability of the proposed method and the results are compared with those obtained from the analytical and finite element solutions. The proposed RPIM has generated results with no oscillations and they are insensitive to Peclet constraints. In order to test the practical applicability and performance of the RPIM, three case studies of contaminant transport through the landfill liners are presented. A good agreement is obtained between the results of the RPIM and the field investigation data.

A non-dimensional theoretical approach to model high-velocity impact on thick woven plates

  • Alonso, L.;Garcia-Gonzalez, D.;Navarro, C.;Garcia-Castillo, S.K.
    • Steel and Composite Structures
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    • v.38 no.6
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    • pp.717-737
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    • 2021
  • A theoretical energy-based model to capture the mechanical response of thick woven composite laminates, which are used in such applications as maritime or aerospace, to high-velocity impact was developed. The dependences of the impact phenomenon on material and geometrical parameters were analysed making use of the Vaschy-Buckingham Theorem to provide a non-dimensional framework. The model was divided in three different stages splitting the physical interpretation of the perforation process: a first where different dissipative mechanisms such as compression or shear plugging were considered, a second where a transference of linear momentum was assumed and a third where only friction took place. The model was validated against experimental data along with a 3D finite element model. The numerical simulations were used to validate some of the new hypotheses assumed in the theoretical model to provide a more accurate explanation of the phenomena taking place during a high-velocity impact.