scholarly journals Hydrodynamic modelling of a regulated Mediterranean coastal lagoon, the Albufera of Valencia (Spain)

2014 ◽  
Vol 16 (5) ◽  
pp. 1062-1076 ◽  
Author(s):  
Javier García Alba ◽  
Aina G. Gómez ◽  
Pilar del Barrio Fernández ◽  
Andrés García Gómez ◽  
César Álvarez Díaz
Keyword(s):  
Coastal Lagoon ◽  
Sea Water ◽  
Numerical Models ◽  
Coastal Lagoons ◽  
Three Dimensional ◽  
Real Data ◽  
Two Dimensional ◽  
Shallow Water Models ◽  
Dimensional Models

Coastal lagoon hydrodynamics are strongly influenced by sea water exchange, especially when the connection between the lagoon and the sea is artificially regulated. These situations increase the complexity of the hydrodynamic regime, requiring the use of numerical models to understand their behaviour. Traditionally, one-dimensional models have been used, although in recent years, the development of two-dimensional shallow water models and advanced numerical techniques have increased notably. However, most of the existing bi-dimensional models consider the connection to the sea as a boundary condition, and they do not take into consideration the sea-lagoon exchange. In this paper, a fully two-dimensional hydrodynamic model of a heavily regulated coastal lagoon, which includes the artificial connection with the sea, is presented. The model allows the characterization of water level variation in the lagoon, taking into account the combined effect of different forcings. This model consists of two hydrodynamic modules: a long wave module (two-dimensional depth-averaged) which includes the analysis of a system of sluice gates, and a wind module (quasi three-dimensional). The model was successfully calibrated and validated with real data, showing its ability to accurately describe the hydraulic dynamics of regulated coastal lagoons.

In Silico Identification and Molecular Characterization of Extracellular Cathepsin L Proteases from Giardia duodenalis

2020 ◽  
Vol 17 (4) ◽  
pp. 342-351
Author(s):  
Sergio A. Durán-Pérez ◽  
José G. Rendón-Maldonado ◽  
Lucio de Jesús Hernandez-Diaz ◽  
Annete I. Apodaca-Medina ◽  
Maribel Jiménez-Edeza ◽  
...  
Keyword(s):  
In Silico ◽  
Cathepsin L ◽  
Three Dimensional ◽  
Giardia Duodenalis ◽  
Evolutionary Genetics ◽  
Extracellular Proteins ◽  
In Silico Identification ◽  
Dimensional Models ◽  
Three Dimensional Models

Background: The protozoan Giardia duodenalis, which causes giardiasis, is an intestinal parasite that commonly affects humans, mainly pre-school children. Although there are asymptomatic cases, the main clinical features are chronic and acute diarrhea, nausea, abdominal pain, and malabsorption syndrome. Little is currently known about the virulence of the parasite, but some cases of chronic gastrointestinal alterations post-infection have been reported even when the infection was asymptomatic, suggesting that the cathepsin L proteases of the parasite may be involved in the damage at the level of the gastrointestinal mucosa. Objective: The aim of this study was the in silico identification and characterization of extracellular cathepsin L proteases in the proteome of G. duodenalis. Methods: The NP_001903 sequence of cathepsin L protease from Homo sapienswas searched against the Giardia duodenalisproteome. The subcellular localization of Giardia duodenaliscathepsin L proteases was performed in the DeepLoc-1.0 server. The construction of a phylogenetic tree of the extracellular proteins was carried out using the Molecular Evolutionary Genetics Analysis software (MEGA X). The Robetta server was used for the construction of the three-dimensional models. The search for possible inhibitors of the extracellular cathepsin L proteases of Giardia duodenaliswas performed by entering the three-dimensional structures in the FINDSITEcomb drug discovery tool. Results: Based on the amino acid sequence of cathepsin L from Homo sapiens, 8 protein sequences were identified that have in their modular structure the Pept_C1A domain characteristic of cathepsins and two of these proteins (XP_001704423 and XP_001704424) are located extracellularly. Threedimensional models were designed for both extracellular proteins and several inhibitory ligands with a score greater than 0.9 were identified. In vitrostudies are required to corroborate if these two extracellular proteins play a role in the virulence of Giardia duodenalisand to discover ligands that may be useful as therapeutic targets that interfere in the mechanism of pathogenesis generated by the parasite. Conclusion: In silicoanalysis identified two proteins in the Giardia duodenalisprotein repertoire whose characteristics allowed them to be classified as cathepsin L proteases, which may be secreted into the extracellular medium to act as virulence factors. Three-dimensional models of both proteins allowed the identification of inhibitory ligands with a high score. The results suggest that administration of those compounds might be used to block the endopeptidase activity of the extracellular cathepsin L proteases, interfering with the mechanisms of pathogenesis of the protozoan parasite Giardia duodenalis.

Mine Impact Burial Prediction From One to Three Dimensions

2008 ◽  
Vol 62 (1) ◽  
Author(s):  
Peter C. Chu
Keyword(s):  
Three Dimensional ◽  
Time History ◽  
Three Dimensions ◽  
Vertical Position ◽  
Burial Depth ◽  
Prediction Errors ◽  
Two Dimensional ◽  
Dimensional Model ◽  
One Dimensional ◽  
Dimensional Models

The Navy’s mine impact burial prediction model creates a time history of a cylindrical or a noncylindrical mine as it falls through air, water, and sediment. The output of the model is the predicted mine trajectory in air and water columns, burial depth/orientation in sediment, as well as height, area, and volume protruding. Model inputs consist of parameters of environment, mine characteristics, and initial release. This paper reviews near three decades’ effort on model development from one to three dimensions: (1) one-dimensional models predict the vertical position of the mine’s center of mass (COM) with the assumption of constant falling angle, (2) two-dimensional models predict the COM position in the (x,z) plane and the rotation around the y-axis, and (3) three-dimensional models predict the COM position in the (x,y,z) space and the rotation around the x-, y-, and z-axes. These models are verified using the data collected from mine impact burial experiments. The one-dimensional model only solves one momentum equation (in the z-direction). It cannot predict the mine trajectory and burial depth well. The two-dimensional model restricts the mine motion in the (x,z) plane (which requires motionless for the environmental fluids) and uses incorrect drag coefficients and inaccurate sediment dynamics. The prediction errors are large in the mine trajectory and burial depth prediction (six to ten times larger than the observed depth in sand bottom of the Monterey Bay). The three-dimensional model predicts the trajectory and burial depth relatively well for cylindrical, near-cylindrical mines, and operational mines such as Manta and Rockan mines.

BIFURCATION SCENARIO OF A THREE-DIMENSIONAL VAN DER POL OSCILLATOR

1993 ◽  
Vol 03 (02) ◽  
pp. 399-404 ◽  
Author(s):  
T. SÜNNER ◽  
H. SAUERMANN
Keyword(s):  
Bifurcation Diagram ◽  
Bifurcation Analysis ◽  
Chaotic Behavior ◽  
Three Dimensional ◽  
Global Bifurcation ◽  
Dynamical Behaviour ◽  
Van Der Pol Oscillator ◽  
Two Dimensional ◽  
Van Der Pol ◽  
Dimensional Models

Nonlinear self-excited oscillations are usually investigated for two-dimensional models. We extend the simplest and best known of these models, the van der Pol oscillator, to a three-dimensional one and study its dynamical behaviour by methods of bifurcation analysis. We find cusps and other local codimension 2 bifurcations. A homoclinic (i.e. global) bifurcation plays an important role in the bifurcation diagram. Finally it is demonstrated that chaos sets in. Thus the system belongs to the few three-dimensional autonomous ones modelling physical situations which lead to chaotic behavior.

LOW TEMPERATURE MODELS OF METAL OXIDE SEMICONDUCTOR FIELD-EFFECT TRANSISTORS

1995 ◽  
Vol 06 (02) ◽  
pp. 317-373 ◽  
Author(s):  
G. GILDENBLAT ◽  
D. FOTY
Keyword(s):  
Low Temperature ◽  
Field Effect Transistors ◽  
Numerical Models ◽  
Three Dimensional ◽  
Oxide Semiconductor ◽  
Characteristic Time Scale ◽  
Mos Transistors ◽  
Short Channel ◽  
Temperature Range ◽  
Dimensional Models

We review the modeling of silicon MOS devices in the 10–300 K temperature range with an emphasis on the specifics of low-temperature operation. Recently developed one-dimensional models of long-channel transistors are discussed in connection with experimental determination and verification of the effective channel mobility in a wide temperature range. We also present analytical pseudo-two-dimensional models of short-channel devices which have been proposed for potential use in circuit simulators. Several one-, two-, and three-dimensional numerical models are discussed in order to gain insight into the more subtle details of the low-temperature device physics of MOS transistors and capacitors. Particular attention is paid to freezeout effects which, depending on the device design and the ambient temperature range, may or may not be important for actual device operation. The numerical models are applied to study the characteristic time scale of freezeout transients in the space-charge regions of silicon devices, to the analysis and suppression of delayed turn-off in MOS transistors with compensated channel, and to the temperature dependence of three-dimensional effects in short-channel, narrow-channel MOSFETs.

Preliminary Ship Design Using One and Two-Dimensional Models

1999 ◽  
Vol 36 (02) ◽  
pp. 102-112
Author(s):  
Michael D. A. Mackney ◽  
Carl T. F. Ross
Keyword(s):  
Finite Element ◽  
Dimensional Analysis ◽  
Three Dimensional ◽  
Two Dimensional ◽  
One Dimensional ◽  
Dimensional Finite Element ◽  
Dimensional Models ◽  
Support Conditions ◽  
The One ◽  
Three Dimensional Finite Element

Computational studies of hull-superstructure interaction were carried out using one-, two-and three-dimensional finite element analyses. Simplification of the original three-dimensional cases to one- and two-dimensional ones was undertaken to reduce the data preparation and computer solution times in an extensive parametric study. Both the one- and two-dimensional models were evaluated from numerical and experimental studies of the three-dimensional arrangements of hull and superstructure. One-dimensional analysis used a simple beam finite element with appropriately changed sections properties at stations where superstructures existed. Two-dimensional analysis used a four node, first order quadrilateral, isoparametric plane elasticity finite element, with a corresponding increase in the grid domain where the superstructure existed. Changes in the thickness property reflected deck stiffness. This model was essentially a multi-flanged beam with the shear webs representing the hull and superstructure sides, and the flanges representing the decks One-dimensional models consistently and uniformly underestimated the three-dimensional behaviour, but were fast to create and run. Two-dimensional models were also consistent in their assessment, and considerably closer in predicting the actual behaviours. These models took longer to create than the one-dimensional, but ran in very much less time than the refined three-dimensional finite element models Parametric insights were accomplished quickly and effectively with the simplest model and processor, but two-dimensional analyses achieved closer absolute measure of the displacement behaviours. Although only static analysis with simple loading and support conditions were presented, it is believed that similar benefits would be found for other loadings and support conditions. Other engineering components and structures may benefit from similarly judged simplification using one- and two-dimensional models to reduce the time and cost of preliminary design.

scholarly journals Experience of employment of computational models for water quality modelling

2019 ◽  
Vol 97 ◽  
pp. 05030 ◽  
Author(s):  
Anatoly Krutov ◽  
Dilshod Bazarov ◽  
Begzod Norkulov ◽  
Bakhtiyar Obidov ◽  
Bobur Nazarov
Keyword(s):  
Computational Models ◽  
Numerical Models ◽  
Qualitative Difference ◽  
Three Dimensional ◽  
Sufficient Conditions ◽  
Aral Sea ◽  
Two Dimensional ◽  
Dimensional Model ◽  
Two Dimensional Model ◽  
Wind Currents

The purpose of the article is to develop the required and sufficient conditions under which numerical methods can be used for engineering calculations and for scientific research of hydrodynamic processes in solving practical problems related to predicting the spread of pollutants in water bodies and streams. The conducted studies consisted in comparing the results of laboratory experiments and mathematical modelling, in particular the distribution of heat in a stream with different temperature in water layers was studied. To check the adequacy of the proposed numerical models, calculations were performed and comparisons were made with the results of experimental data. The obtained results allowed to determine the boundaries of the qualitative difference in the flow behaviour for different numbers of Froude and Reynolds. The accuracy of the method was also studied. A number of additional requirements for numerical models were proposed in addition to approcsimation and stability, such as requirements of conservativeness (divergence), existence of trivial solutions on grids, possibility to calculate highly unsteady, quasi-stable, pulsating and stationary flows, requirement of invariance of linearized equations, as well as the requirement of a one-dimensional scheme to be a consequence of a two-dimensional scheme. Distribution of velocities of wind currents using a three-dimensional and two-dimensional model was studied for a real object. A shallow-water bay of the Aral Sea was chosen as the object for the research. Comparison of the calculation results for both models showed that the flow velocity fields, as well as the distribution of pollutants in shallow waters, can be performed using a two-dimensional model.

Three-Dimensional Strain-Based Model for the Severity Characterization of Dented Pipelines

2018 ◽  
Vol 1 (3) ◽  
Author(s):  
Chike Okoloekwe ◽  
Muntaseer Kainat ◽  
Doug Langer ◽  
Sherif Hassanien ◽  
J.J. Roger Cheng ◽  
...  
Keyword(s):  
Oil And Gas ◽  
Numerical Models ◽  
Three Dimensional ◽  
Strain Analysis ◽  
Computation Time ◽  
Order Continuity ◽  
Element Analysis ◽  
The Mathematical Model ◽  
Derivatives Of

Oil and gas pipelines traverse long distances and are often subjected to mechanical forces that result in permanent distortion of its geometric cross section in the form of dents. In order to prioritize the repair of dents in pipelines, dents need to be ranked in order of severity. Numerical modeling via finite element analysis (FEA) to rank the dents based on the accumulated localized strain is one approach that is considered to be computationally demanding. In order to reduce the computation time with minimal effect to the completeness of the strain analysis, an approach to the analytical evaluation of strains in dented pipes based on the geometry of the deformed pipe is presented in this study. This procedure employs the use of B-spline functions, which are equipped with second-order continuity to generate displacement functions, which define the surface of the dent. The strains associated with the deformation can be determined by evaluating the derivatives of the displacement functions. The proposed technique will allow pipeline operators to rapidly determine the severity of a dent with flexibility in the choice of strain measure. The strain distribution predicted using the mathematical model proposed is benchmarked against the strains predicted by nonlinear FEA. A good correlation is observed in the strain contours predicted by the analytical and numerical models in terms of magnitude and location. A direct implication of the observed agreement is the possibility of performing concise strain analysis on dented pipes with algorithms relatively easy to implement and not as computationally demanding as FEA.

scholarly journals Characterization of the translocon of the outer envelope of chloroplasts

2003 ◽  
Vol 160 (4) ◽  
pp. 541-551 ◽  
Author(s):  
Enrico Schleiff ◽  
Jürgen Soll ◽  
Michael Küchler ◽  
Werner Kühlbrandt ◽  
Roswitha Harrer
Keyword(s):  
Three Dimensional ◽  
Dependent Manner ◽  
Interior Structure ◽  
Two Dimensional ◽  
Outer Envelope ◽  
Core Complex ◽  
The Core ◽  
Precursor Proteins ◽  
Stable Core

The protein translocon of the outer envelope of chloroplasts (Toc) consists of the core subunits Toc159, Toc75, and Toc34. To investigate the molecular structure, the core complex was purified. This core complex has an apparent molecular mass of ∼500 kD and a molecular stoichiometry of 1:4:4–5 between Toc159, Toc75, and Toc34. The isolated translocon recognizes both transit sequences and precursor proteins in a GTP-dependent manner, suggesting its functional integrity. The complex is embedded by the lipids phosphatidylcholine and digalactosyldiacylglyceride. Two-dimensional structural analysis by EM revealed roughly circular particles consistent with the formation of a stable core complex. The particles show a diameter of ∼130 Å with a solid ring and a less dense interior structure. A three-dimensional map obtained by random conical tilt reconstruction of electron micrographs suggests that a “finger”-like central region separates four curved translocation channels within one complex.

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