Domain Length Research Articles

Statistical Analysis on The Near-Wake Region of RANS Turbulence Closure Models for Vertical Axis Tidal Turbine

The flow field in the near wake region (up to six turbine diameters downstream) of a tidal current turbine is strongly driven by the combined wake of the device support structure and the rotor. Accurate characterisation of the near-wake region is important, but it is dominated by highly turbulent, slow-moving fluid. At present, limited number of research has been undertaken into the characterisation of the near-wake region for a Vertical Axis Tidal Turbine (VATT) device using the Reynolds Averaged Navier Stokes (RANS) model in the shallow water environment of Malaysia. This paper presents a comprehensive statistical analysis using the Mean Absolute Error (MEA), Mean Squared Error (MSE) and Root Mean Squared Error (RMSE) on the near-wake region for shallow water application by comparing numerical solutions (i.e., different types of RANS turbulence models using Ansys Fluent) with published experimental data. Seven RANS turbulence models with a single VATT, represented by using a cylindrical object, were employed in the preliminary study. The statistical analysis performed in this study is essential in exploring and giving a detailed understanding on the most suitable RANS turbulence model to be improved, specifically on its near-wake region. In this study, the near wake region is defined as D ≤ 6, where D is the device diameter. The analysis shows that the RANS numerical solutions are unable to accurately replicate the near-wake region based on large statistical errors computed. The average RMSE of near-wake region at z/D = [2, 3, 4, 6] are 0.5864, 0.4127, 0.4344 and 0.3577 while the average RMSE at far-wake region z/D = [8, 12] are 0.2269 and 0.1590, where z is the distance from the cylindrical object along the length of domain. The statistical error values are found to decrease with increasing downstream distance from a cylindrical object. Notably, the standard k–ε and realizable k–ε models are the two best turbulent models representing the near-wake region in RANS modelling, yielding the lowest statistical errors (RMSE at z/D = [2, 3, 4, 6] are 0.5666, 0.4020, 0.4113 and 0.3455) among the tested parameters

Abnormal Domain Growth during Polarization Reversal in Lithium Niobate Crystal Modified by Proton Exchange

The results of an experimental study of the abnormal domain structure kinetics in lithium niobate single crystals with a surface layer modified by soft proton exchange are presented. Domain switching in a wide field range allowed two qualitatively different types of domain structure evolution to be revealed: (1) the traditional growth of hexagonal domains in fields higher than 21.5 kV/mm and (2) the abnormal growth of stripe domains oriented along the Y crystallographic directions in the field range from 3.8 to 21.5 kV/mm. The stripe domains had a width up to 4 µm and depth up to 30 µm. It was shown that the time dependence of the total length of stripe domains could be analyzed in terms of the modified Kolmogorov–Avrami approach, taking into account the transition from the one-dimensional β-model to the one-dimensional α-model. The possibility of the controllable creation of a quasi-periodic structure of stripe domains with an average period of 5 µm by a two-stage polarization switching process was demonstrated. The formation and growth of stripe domains were considered in terms of the kinetic approach to the evolution of the domain structure as a result of the domain walls’ motion under inefficient screening conditions caused by the presence of a modified surface layer. The abnormally low threshold fields were attributed to a presence of a “built-in” field facilitating switching, created by a composition gradient induced by soft proton exchange.

On the role of membrane embedding, protein rigidity and transmembrane length in lipid membrane fusion.

The fusion of biological membranes is ubiquitous in natural processes like exo- and endocytosis, intracellular trafficking and viral entry. Membrane fusion is also utilized in artificial biomimetic fusion systems, e.g. for drug delivery. Both the natural and the biomimetic fusion systems rely on a wide range of (artificial) proteins mediating the fusion process. Although the exact mechanisms of these proteins differ, clear analogies in their general behavior can be observed in bringing the membranes in close proximity and mediating the fusion reaction. In our study, we use molecular dynamics simulations with coarse grained models, mimicking the general behavior of fusion proteins (spikes), to systematically examine the effects of specific characteristics of these proteins on the fusion process. The protein characteristics considered are (i) the type of membrane embedding, i.e., either transmembrane or not, (ii) the rigidity, and (iii) the transmembrane domain (TMD) length. The results show essential differences in fusion pathway between monotopic and transmembrane spikes, in which transmembrane spikes seem to inhibit the formation of hemifusion diaphragms, leading to a faster fusion development. Furthermore, we observed that an increased rigidity and a decreased TMD length both proved to contribute to a faster fusion development. Finally, we show that a single spike may suffice to successfully induce a fusion reaction, provided that the spike is sufficiently rigid and attractive. Not only does this shed light on biological fusion of membranes, it also provides clear design rules for artificial membrane fusion systems.

Barycentric Lagrange Interpolation Methods for Evaluating Singular Integrals

We investigate new, straightforward methods for interpolating and integrating discontinuous single and two-variable real valued functions. The method is based on some modified matrix–vector barycentric Lagrange interpolation formulas. We developed seven rules for the optimum distribution of nodes inside the domain of integration: five for single-valued discontinuous functions, and two rules for the two independent variables of discontinuous functions. We designed these rules to depend on the length of the integration domain and the degree of the interpolant polynomials. Thus, we obtained uniform interpolation and minimum roundoff errors. Based on these rules with the application of the modified matrix–vector barycentric formulas, we easily isolated the singularities of the interpolant integrands and evaluated the corresponding interpolant integral values with super accuracy. The obtained numerical solutions of the five given examples show the high accuracy and efficiency of the presented method compared with the exact solutions and with the cited method.

Two stability results for the Kawahara equation with a time-delayed boundary control

In this paper, we consider the Kawahara equation in a bounded interval and with a delay term in one of the boundary conditions. Using two different approaches, we prove that this system is exponentially stable under a condition on the length of the spatial domain. Specifically, the first result is obtained by introducing a suitable energy and using the Lyapunov approach, to ensure that the unique solution of the Kawahara system exponentially decays. The second result is achieved by means of a compactness-uniqueness argument, which reduces our study to prove an observability inequality. Furthermore, the main novelty of this work is to characterize the critical set phenomenon for this equation by showing that the stability results hold whenever the spatial length is related to the M\"obius transformations.

Two alternative splicing variants of a wheat gene TaNAK1, TaNAK1.1 and TaNAK1.2, differentially regulate flowering time and plant architecture leading to differences in seed yield of transgenic Arabidopsis.

In wheat production, appropriate flowering time and ideal plant architecture are the prerequisites for high grain yield. Alternative splicing (AS) is a vital process that regulates gene expression at the post-transcriptional level, and AS events in wheat have been found to be closely related to grain-related traits and abiotic stress tolerance. However, AS events and their biological roles in regulating flowering time and plant architecture in wheat remain unclear. In this study, we report that TaNAK1 undergoes AS, producing three splicing variants. Molecular characterization of TaNAK1 and its splicing variants demonstrated that all three protein isoforms have a conserved NB-ARC domain and a protein kinase domain, but the positions of these two domains and the length of the protein kinase domains are different among them, implying that they may have different three-dimensional structures and therefore have different functions. Further investigations showed that the two splicing variants of TaNAK1, TaNAK1.1 and TaNAK1.2, exhibited different expression patterns during wheat growth and development, while the other one, TaNAK1.3, was not detected. Subcellular localization demonstrated that TaNAK1.1 was mainly localized in the cytoplasm, while TaNAK1.2 was localized in the nucleus and cytoplasm. Both TaNAK1.1 and TaNAK1.2 exhibit protein kinase activity in vitro. Ectopic expression of TaNAK1.1 and TaNAK1.2 in Arabidopsis demonstrated that these two splicing variants play opposite roles in regulating flowering time and plant architecture, resulting in different seed yields. TaNAK1.2 positive regulates the transition from vegetative to reproductive growth, plant height, branching number, seed size, and seed yield of Arabidopsis, while TaNAK1.1 negatively regulates these traits. Our findings provide new gene resource for regulating flowering time and plant architecture in crop breeding for high grain yield.

Fine Mapping and Identification of a Candidate Gene of Downy Mildew Resistance, RPF2, in Spinach (Spinacia oleracea L.)

Downy mildew is a major threat to the economic value of spinach. The most effective approach to managing spinach downy mildew is breeding cultivars with resistance genes. The resistance allele RPF2 is effective against races 1-10 and 15 of Peronospora farinosa f. sp. Spinaciae (P. effusa) and is widely used as a resistance gene. However, the gene and the linked marker of RPF2 remain unclear, which limit its utilization. Herein, we located the RPF2 gene in a 0.61 Mb region using a BC1 population derived from Sp39 (rr) and Sp62 (RR) cultivars via kompetitive allele specific PCR (KASP) markers. Within this region, only one R gene, Spo12821, was identified based on annotation information. The amino acid sequence analysis showed that there were large differences in the length of the LRR domain between the parents. Additionally, a molecular marker, RPF2-IN12821, was developed based on the sequence variation in the Spo12821, and the evaluation in the BC1 population produced a 100% match with resistance/susceptibility. The finding of the study could be valuable for improving our understanding of the genetic basis of resistance against the downy mildew pathogen and breeding resistance lines in the future.

Enabling direct kinetic simulation of dense plasma plume expansion for laser ablation plasma thrusters

Laser ablation plasma thrusters are an emerging space propulsion concept that provides promise for lightweight payload delivery. Predicting the lifetime and performance of these thrusters hinges on a comprehensive characterization of the expansion dynamics of the ablated plasma plume. While state-of-the-art techniques for simulating plasmas are often particle-based, a grid-based direct kinetic solver confers advantages in such a transient and inhomogeneous problem by eliminating statistical noise. A direct kinetic solver including interparticle collisions is employed on a plume expansion model problem spanning one dimension each in configuration and velocity space. The high degree of thermodynamic nonequilibrium inherent in plume expansion is characterized, justifying the need for a kinetic rather than a hybrid or fluid solver. Thruster-relevant metrics such as the momentum flux are also computed. The plume dynamics are observed to be highly inhomogeneous in space with insufficient time for thermalization in the region preceding the expansion front, and the theoretical possibility of reducing the local grid resolution by up to two orders of magnitude at the far end of the domain is established. These grid-point requirements are verified via the employment of nonuniform grids of various expansion ratios, several of which also employ coarsening in velocity space. Longer domain lengths are explored to characterize thruster-scale phenomena and larger ambient pressures are simulated as a testbed to probe facility effects due to collisions with background particles.

Phase separation and aging dynamics of binary liquids in porous media

We employ the state-of-the-art molecular dynamics simulations to study the kinetics of phase separation and aging phenomena of segregating binary fluid mixtures imbibed in porous materials. Different random porous structures are considered to understand the effect of pore morphology on coarsening dynamics. We find the effect of complex geometrical confinement resulting in the dramatic slowing down in the phase separation dynamics. The domain growth follows the power law with an exponent dependent on the porous host structure. After the transient period, a crossover to a slower domain growth is observed when the domain size becomes comparable to the pore size. Due to the geometric confinement, the correlation function and structure factor modify to a non-Porod behavior and violate the superuniversality hypothesis. The role of porous host structure on the nonequilibrium aging dynamics is studied qualitatively by computing the two-time order-parameter autocorrelation function. This quantity exhibits scaling laws with respect to the ratio of the domain length at the observation time and the age of the system. We find the scaling laws hold well for such confined segregating fluid mixtures.

Accurate Stall Prediction for Thick Airfoil by Delayed Detached-Eddy Simulations

The continuous increase in wind turbine blade length raises a serious question about how to effectively reduce the blade mass. As one of the solutions, recently, some wind turbine manufacturers are moving towards longer blades with thicker airfoils. As most of the numerical simulation experiences are based on thin airfoils, the present paper focused on airfoils with thickness to chord ratios of 30% and specifically focused on the influence of spanwise length on the numerical results. Airfoils with a spanwise length of 0.1 to 5 chords were simulated utilizing the Delayed Detached-Eddy Simulations (DDES) approach. One of the important objectives was to identify the necessary grid resolution and configuration while still maintaining accuracy under a deep stall situation. It was found that the spanwise length of the computational domain had a crucial influence on the prediction of lift and drag. At a stall angle of attack, the aerodynamic force could not be accurately predicted when the airfoil span was reduced to 0.3 chords, even with a high grid density. The periodicity of the spanwise flow was clearly visible when the airfoil span was extended to 5 chords.

Reconstruction of Zigzag Graphene Edges: Energetics, Kinetics, and Residual Defects.

Ab initio calculations are performed to study consecutive reconstruction of a zigzag graphene edge. According to the obtained energy profile along the reaction pathway, the first reconstruction step, formation of the first pentagon-heptagon pair, is the slowest one, while the growth of an already nucleated reconstructed edge domain should occur steadily at a much higher rate. Domains merge into one only in 1/4 of cases when they get in contact, while in the rest of the cases, residual defects are left. Structure, energy, and magnetic properties of these defects are studied. It is found that spontaneous formation of pairs of residual defects (i.e., spontaneous domain nucleation) in the fully reconstructed edge is unlikely at temperatures below 1000 K. Using a kinetic model, we show that the average domain length is several micrometers at room temperature and it decreases exponentially upon increasing the temperature at which the reconstruction takes place.

Single-Crystalline Imine-Linked Two-Dimensional Covalent Organic Frameworks Separate Benzene and Cyclohexane Efficiently.

Two-dimensional (2D) covalent organic frameworks (COFs) are composed of structurally precise, permanently porous, layered macromolecular sheets, which are traditionally synthesized as polycrystalline solids with crystalline domain lengths smaller than 100 nm. Here, we polymerize imine-linked 2D COFs as suspensions of faceted single crystals in as little as 5 min at moderate temperature and ambient pressure. Single crystals of two imine-linked 2D COFs were prepared, consisting of a rhombic 2D COF (TAPPy-PDA) and a hexagonal 2D COF (TAPB-DMPDA). The sizes of TAPPy-PDA and TAPB-DMPDA crystals were tuned from 720 nm to 4 μm and 450 nm to 20 μm in width, respectively. High-resolution transmission electron microscopy revealed that the COF crystals consist of layered, 2D polymers comprising single-crystalline domains. Continuous rotation electron diffraction resolved the unit cell and crystal structure of both COFs, which are single-crystalline in the a-b plane but disordered in the stacking c dimension. Single crystals of both COFs were incorporated into gas chromatography separation columns and exhibited unusual selective retention of cyclohexane over benzene, with single-crystalline TAPPy-PDA significantly outperforming single-crystalline TAPB-DMPDA. Polycrystalline TAPPy-PDA exhibited no separation, while polycrystalline TAPB-DMPDA exhibited poor separation and the opposite order of elution, retaining benzene more than cyclohexane, indicating the importance of improved material quality for COFs to exhibit properties that derive from their precise, crystalline structures. This work represents the first example of synthesizing imine-linked 2D COF single crystals at ambient pressure and short reaction times and demonstrates the promise of high-quality COFs for molecular separations.

Adaptive observer design for uncertain nonlinear ODE‐PDE cascades

SummaryWe are revisiting the problem of adaptive observer design for systems that are constituted of an Ordinary Differential Equation (ODE), containing a globally Lipschitz function of the state, and a linear Partial Differential Equation (PDE) of a diffusion–reaction heat type. The ODE and PDE are connected in series and both are subject to parametric uncertainties. In addition to nonlinearity and uncertainty, the system complexity also lies in the fact that no sensor can be implemented at the junction point between the ODE and the PDE. In the absence of parameter uncertainty, nonadaptive state observers are available featuring exponential convergence. However, convergence is guaranteed only under the condition that either the Lipschitz coefficient is sufficiently small or the PDE domain length is sufficiently small. To get around this limitation, and also to account for parameter uncertainty, we develop a design that involves two concatenated adaptive observers, covering the two subintervals of the PDE domain. The proposed design employs one extra sensor, providing the measurement of the PDE state at an inner position close to the ODE‐PDE junction point. Both observers are shown to be exponentially convergent, under ad‐hoc persistent excitation (PE) conditions, with no limitation on the Lipschitz coefficient and domain length.

Chemoenzymatic Synthesis of Heparan Sulfate Oligosaccharides having a Domain Structure**

AbstractHeparan sulfate (HS) has a domain structure in which regions that are modified by epimerization and sulfonation (NS domains) are interspersed by unmodified fragments (NA domains). There is data to support that domain organization of HS can regulate binding of proteins, however, such model has been difficult to probe. Here, we report a chemoenzymatic methodology that can provide HS oligosaccharides composed of two or more NS domains separated by NA domains of different length. It is based on the chemical synthesis of a HS oligosaccharide that enzymatically was extended by various GlcA‐GlcNAc units and terminated in GlcNAc having an azido moiety at C‐6 position. HS oligosaccharides having an azide and alkyne moiety could be assembled by copper catalyzed alkyne‐azide cycloaddition to give compounds having various NS domains separated by unsulfonated regions. Competition binding studies showed that the length of an NA domain modulates the binding of the chemokines CCL5 and CXCL8.

Chemoenzymatic Synthesis of Heparan Sulfate Oligosaccharides having a Domain Structure.

Heparan sulfate (HS) has a domain structure in which regions that are modified by epimerization and sulfonation (NS domains) are interspersed by unmodified fragments (NA domains). There is data to support that domain organization of HS can regulate binding of proteins, however, such model has been difficult to probe. Here, we report a chemoenzymatic methodology that can provide HS oligosaccharides composed of two or more NS domains separated by NA domains of different length. It is based on the chemical synthesis of a HS oligosaccharide that enzymatically was extended by various GlcA-GlcNAc units and terminated in GlcNAc having an azido moiety at C-6 position. HS oligosaccharides having an azide and alkyne moiety could be assembled by copper catalyzed alkyne-azide cycloaddition to give compounds having various NS domains separated by unsulfonated regions. Competition binding studies showed that the length of an NA domain modulates the binding of the chemokines CCL5 and CXCL8.

Water Transport Characteristics of Multiple Structures of Xylem Vessels in Magnolia

The multiple structures of xylem vessels in Magnolia provide stable and efficient water transport channels. The structural parameters of xylem vessels were studied in wood sections and in macerated materials. The results showed that the xylem vessels of Magnolia contained a helical thickening structure and a pit structure of a secondary wall, and the end walls had a scalariform perforation plate. The helical thickening and scalariform perforation plate increased the flow resistance of the vessel, and the pit structure decreased the flow resistance of the vessel. There was a close positive correlation between the flow resistance of the vessels and the helical width, the helical height, the thickness of the scalariform perforation plate, the number of holes in the scalariform perforation plate, the length of the pit canal, and the pit spacing. In addition, there was a negative correlation between the flow resistance of the vessels and the helical spacing, the pit vertical diameter, and the pit domain length. Among these structural parameters, the helical height, the number of holes, and the length of pit canal had a greater influence on the flow resistance. The pit structure caused the vessel to produce radial water transport. The radial transmission efficiency increased with the increase in the pit domain length. With no pit membrane in the pit structure of Magnolia, the radial transmission efficiency would be between 43.99% and 53.21%.

Exactly equivalent thermal conductivity in finite systems from equilibrium and nonequilibrium molecular dynamics simulations

In a previous paper (Dong et al., 2021), we showed that the equilibrium molecular dynamics (EMD) method can be used to compute the apparent thermal conductivity of finite systems. It has been shown that the apparent thermal conductivity from EMD for a system with domain length 2 L is equal to that from nonequilibrium molecular dynamics (NEMD) for a system with domain length L . Taking monolayer silicene with an accurate machine learning potential as an example, here we show that the thermal conductivity values from EMD and NEMD agree for the same domain length if the NEMD is applied with periodic boundary conditions in the transport direction. Our results thus establish an exact equivalence between EMD and NEMD for thermal conductivity calculations. • Large-scale MD simulations are performed with an accurate machine learned potential. • Exactly equivalent thermal conductivity in EMD and NEMD has been established. • The exact equivalence is explained in terms of phonon-boundary scattering. • We suggest that EMD serves as a feasible alternative method to NEMD in finite systems.

Deciphering the individual effects of the fluid flow and material evaporation physics on the melting characteristics and the re-solidification parameters during laser melting of solid Ti6Al4V substrate

• Underlined individual effects of fluid flow and material evaporation separately. • Effect of adding various physics on the computational time consumption presented. • Four different models have been investigated for laser melting of Ti6Al4V. • Optimal numerical model for laser melting has been identified. • Detailed discussion on the solidification parameters in melt pool presented. In this study, the effect of inclusion of fluid flow and material evaporation physics in the thermal models of the laser melting process for Ti6Al4V has been compared to evaluate their individual influence on the simulation results and computational resources consumed. Though the study seems basic, it aims to address the important issue of increase in the computational resources consumption and time when these physics are added to the model. The study also focuses upon finding an optimized model that can enable faster prediction of thermal and melt pool dimension results for macro-scale laser melting cases, while ensuring the accuracy of these results against the experimental observations. It was seen that the fluid flow and material evaporation assisted each other in some aspects and opposed in some others, but the extent of their individual effects varied significantly in the magnitudes. Along with the individual melt pool characteristics comparison, the thermal field along the length, width and depth of the computational domain as well as the computational time consumed by each simulation are also compared for different models. It is obtained through experimental validation that material evaporation could reduce the reliance on the fluid flow inclusion in the model to accurately predict the melt pool dimensions, that too while consuming drastically less computational time. Through these comparisons and experimental validation, an optimized model has been identified, which is then used to present a parametric analysis of the solidification variables (G, R, GR and G/R) for the laser melting of Ti6Al4V.

Quantification of Soil Sensitivity to Water Erosion by the RUSLE Model in the Oued Amter Watershed, Northwestern Morocco

The present study aims to estimate the soil losses in the watershed of Oued Amter extends the length of the internal Rifain domain, located in the region of Tangier-Tetouan-Al Houceima, Chefchaouen province in north-western Morocco. The spatialization of the empirical model was based on the integration of five factors in the Geographic Information System, namely, rainfall erosivity, soil erodibility, vegetation cover, topography and anti-erosion practices, and whose superposition allowed the elaboration of the quantitative map of soil losses at the watershed scale. The Oued Amter watershed covers an area of 300 km2 ; it is elongated with an altitude ranging from 0 m to 2100 m from north to south and a slope that varies from 0 to 58.58%. The rainfall study of the climatic stations located near the watershed has shown the irregularity of rainfall in time and space. The erosivity factor R presented values ranging from 1637.09 to 1937.61, with an average of 1787.35 Mj.mm/ha. h. an (Millijoule. Millimeters/hectare. Hour. Year). The erodibility factor K presents values from 0.139 to 0.140 and it showed that the soils little evolved and the Vertisols are the most vulnerable to erosion.

Comparison of turbulent inflow conditions for neutral stratified atmospheric boundary layer flow

In the present work, measurements of the atmospheric boundary layer (ABL) flow, reproduced in a boundary layer wind tunnel, and large eddy simulation (LES) of the full scale ABL are presented for two ground roughness lengths. In the numerical part the ABL is simulated by utilizing the cyclic boundary conditions in downstream direction and artificial turbulence specified at the inlet. Five synthetic turbulence generation techniques are used with reviewing two input methods for the Reynolds stress. Convergence of mean velocity and second order moments is discussed for various horizontal and vertical grid refinement as well as for different roughness and wall boundary conditions of the ground. The transition of mean velocity, second order moments, stream-wise velocity spectrum and longitudinal turbulent length scale in downstream direction is analyzed. The applicability of the synthetic turbulence condition was confirmed for the LES of ABL simulations. In this way, the inflow domain length for simulations can significantly be reduced.