Water Model Research Articles

A Godunov-type scheme for the Saint-Venant-Exner equations with a moving steady states

The Saint-Venant-Exner system is widely used in industrial codes to model the transport of bed sediments. In practice, most of the methods used for its numerical resolution suffer from significant stability problems due to the fact that they are mainly guaranteed by separation techniques which allow weak coupling between hydraulic and morphodynamic software. The search for an adequate alternative method to this problem is a focus towards which several approaches converge. Recently, many authors have proposed acceptable methods but they are not so trivial to implement in an industrial context and some do not take into account all aspects such as mobile steady states. In this work, we derive a well-balanced scheme that takes into account all stable states, to approach weak solutions of the sediment transport model in shallow waters. We demonstrate that it captures exactly all regular steady solutions with non-evanescent velocities, retains water level positivity and is able to degenerate to a classical shallow water model when the sedimentary transport flow is null. A number of numerical test cases are also presented to illustrate these properties.

Molecular Dynamics Calculation of Interfacial Tension in a Two-Phase Liquid Hydrocarbon–Water–Surfactant System: From Rarefied to Superdense Surfactant Monolayer

A method is proposed for calculating low interfacial tension (IFT) based on molecular dynamics simulation of systems with superdense packing of surfactant molecules at the water–liquid hydrocarbon interface. The interfacial tension was calculated by the molecular dynamics method using the all-atom and coarse-grained models in water–alkane (decane, dodecane) two-phase systems in the presence of various individual surfactants. The following ionic and nonionic surfactants were considered: sodium dodecyl sulfate (SDS), cetyltrimethylammonium chloride (CTAC), sodium dodecylbenzenesulfonate (SDBS), sodium decet-6 sulfate C10E6SO4Na, hexaethylene glycol monodecyl ether (C10E6), triethylene glycol monononadecyl ether (C19E3), and octapropoxypentaethylene glycol monododecyl ether (C12P8E5). It was shown that the interfacial tension decreases to zero when surfactant adsorption increases to the limiting values.

Analysis of Inherent Frequencies to Mitigate Liquid Sloshing in Overhead Double-Baffle Damper

A disco-rectangular volume-fraction-of-fluid (VOF) model tank of a prismatic size is considered here for investigating the severe effect of overhead baffles made of three different materials, nylon, polyamide, and polylactic acid. In this work, the overdamped, undamped, and nominal damped motion of baffles and their effect are studied. In this research, the behaviour of different material baffles based on the sloshing effect and natural frequency of each baffle excited in damped, undamped, and overdamped cases is studied. VOF modelling is carried out in moving Yeoh model mesh with fluid–structure interaction between the water models for various baffle plates. The results of the water volume distribution and baffle displacement operating between a sloshing time of 0 and 1 s are recorded. Also, a strong investigation is carried out for the water volume suspended on overhead baffles by three different material selections.

Assignment of a Physical Energy Scale for the Dimensionless Interaction Energies within the PRIME20 Peptide Model.

We present a calibration scheme to determine the conversion factors from a coarse-grained stochastic approximation Monte Carlo approach using the PRIME20 peptide interaction model into atomistic force-field interaction energies at full explicit aqueous solvation. The conversion from coarse-grained to atomistic structures was done according to our previously established inverse coarse-graining protocol. We provide a physical energy scale for both the backbone hydrogen bonding interactions and the sidechain interactions by correlating the dimensionless energy descriptors of the PRIME20 model with the energies averaged over molecular dynamics simulations. The conversion factor for these interactions turns out to be around 2kJ/mol for the backbone interactions, and zero for the sidechain interactions. We discuss these surprisingly small values in terms of their molecular interpretation.

Ab initio electronic absorption spectra of para-nitroaniline in different solvents: Intramolecular charge transfer effects.

Intramolecular charge transfer (ICT) effects of para-nitroaniline (pNA) in eight solvents (cyclohexane, toluene, acetic acid, dichloroethane, acetone, acetonitrile, dimethylsulfoxide, and water) are investigated extensively. The second-order algebraic diagrammatic construction, ADC(2), ab initio wave function is employed with the COSMO implicit and discrete multiscale solvation methods. We found a decreasing amine group torsion angle with increased solvent polarity and a linear correlation between the polarity and ADC(2) transition energies. The first absorption band involves π → π* transitions with ICT from the amine and the benzene ring to the nitro group, increased by 4%-11% for different solvation models of water compared to the vacuum. A second band of pNA is characterized for the first time. This band is primarily a local excitation on the nitro group, including some ICT from the amine group to the benzene ring that decreases with the solvent polarity. For cyclohexane, the COSMO implicit solvent model shows the best agreement with the experiment, while the explicit model has the best agreement for water.

Density functional modeling of ternary Am(III) hydroxo complexes with Ca or Mg counterions. Do Mg stabilized species exist?

We carried out density functional computations to investigate experimentally suggested ternary Ca–Am(III)–OH and possible Mg–Am(III)–OH complexes in water. We confirmed the experimental stoichiometry for the Ca complexes and their relative stability. For the Mg complexes, we find comparable or weaker complexation. This finding is in agreement with experimental observations. We demonstrate that explicit solvation of counterions is important when comparing Ca and Mg species. For the Ca complexes this has a minimal effect on their relative stability. Contrariwise, Mg complexes exhibit a lower stability and are highly sensitive to explicit short-range solvation effects. Explicit Mg2+ solvation significantly altered both absolute and relative formation energies compared to a simpler model. These findings highlight the crucial role of incorporating explicit short-range solvation effects in accurate computational modeling when small and highly charged ions are treated.

Role of the structural order of the hydration layer in regulating the heterogeneous ice nucleation efficiency

Understanding the complex microscopic mechanisms of heterogeneous ice nucleation is crucial across diverse fields from cloud science to microbiology. In this work, we examined the ability of solid surfaces to promote ice nucleation as a function of the structural order of interfacial water, including the first and second hydration layers. Comprehensive all-atom molecular dynamics simulations using the TIP4P/ice water model were conducted on a water film atop a modeled surface inspired by the (0001) surface of AgI crystal, with varying surface charges. These simulations revealed non-monotonic nucleation rates. The first hydration layer formed a hexagonal hydrogen-bond network resembling ice structures, exhibiting low mobility essential for inducing ice nucleation. Notably, the second hydration layer, acting as a key-point bridge, displayed varying degrees of orientational preference facilitated by inter-layer hydrogen bonds. The calculation of fluctuation parameters indicated that the greater structural order of the second layer significantly enhances the surface’s ice-forming capabilities. Unlike previous studies that focused primarily on the role of the first layer of interfacial water, our findings demonstrate that the second layer provides a more accurate indicator of ice nucleation capabilities.

Effect of the Tundish Inhibitor Design on the Flotation Efficiency of Nonmetallic Inclusions: Water Modeling and Mathematical Simulations by the Reynolds Stress Model

Effect of the Tundish Inhibitor Design on the Flotation Efficiency of Nonmetallic Inclusions: Water Modeling and Mathematical Simulations by the Reynolds Stress Model

Structural characterization of DNA-binding domain of essential mammalian protein TTF 1.

Transcription Termination Factor 1 (TTF1) is a multifunctional mammalian protein with vital roles in various cellular processes, including Pol I-mediated transcription initiation and termination, pre-rRNA processing, chromatin remodelling, DNA damage repair, and polar replication fork arrest. It comprises two distinct functional regions; the N-terminal regulatory region (1-445 aa), and the C-terminal catalytic region (445-859 aa). The Myb domain located at the C-terminal region is a conserved DNA binding domain spanning from 550 to 732 aa (183 residues). Despite its critical role in various cellular processes, the physical structure of TTF1 remains unsolved. Attempts to purify the functional TTF1 protein have been unsuccessful till date. Therefore, we focused on characterizing the Myb domain of this essential protein. We started with predicting a 3-D model of the Myb domain using homology modelling, and ab-initio method. We then determined its stability through MD simulation in an explicit solvent. The model predicted is highly stable, which stabilizes at 200ns. To experimentally validate the computational model, we cloned and expressed the codon optimized Myb domain into a bacterial expression vector and purified the protein to homogeneity. Further, characterization of the protein shows that, Myb domain is predominantly helical (65%) and is alone sufficient to bind the Sal Box DNA. This is the first-ever study to report a complete in silico model of the Myb domain, which is physically characterized. The above study will pave the way towards solving the atomic structure of this essential mammalian protein.

Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects.

Among azobenzene derivatives, azothiophenes represent a relatively recent family of compounds that exhibit similar characteristics as dyes and photoreactive systems. Their technological applications are extensive thanks to the additional design flexibility conferred by the heteroaromatic ring. In this study, we present a comprehensive investigation of the structural and electronic properties of novel dyes derived from 3-thiophenamine, utilizing a multilevel approach. We thoroughly examined the potential energy surfaces of the E and Z isomers for three molecules, each bearing different substituents on the phenyl ring at the para position relative to the diazo group. This exploration was conducted through quantum chemistry calculations at various levels of theory, employing a continuum solvent model. Subsequently, we incorporated an explicit solvent (a dimethyl sulfoxide-water mixture) to simulate the most stable isomers using classical molecular dynamics, delivering a clear picture of the local solvation structure and intermolecular interactions. Finally, a hybrid quantum mechanics/molecular mechanics (QM/MM) approach was employed to accurately describe the evolution of the solutes' properties within their environment, accounting for finite temperature effects.

NP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat.

Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer's disease. Using all-atom molecular dynamics simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289, and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termed nP-collab (for nphosphate collaboration, with n being an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations and is likely to impact the peptide overall dynamics and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidue spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one-six residues apart. Three new metrics specifically tailored for IDPs (proteic Menger curvature, local curvature, and local flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.

Differential scanning calorimetry of proteins and Zimm–Bragg model in water

Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. Hydrogen bonds play a crucial role in stabilizing the three-dimensional structure of proteins. Naturally, information about the strength of hydrogen bonds is contained in the measured DSC profiles. Despite its obvious importance, there is no approach that would allow the extraction of such information from the heat capacity measurements. In order to connect the measured profile to microscopic properties of a polypeptide chain, a proper model is required to fit. Using recent advances in the Zimm–Bragg (ZB) theory of protein folding in water, we propose a new and efficient algorithm to process the DSC experimental data and to extract the H-bonding energy among other relevant constants. Thus, for the randomly picked set of 33 proteins, we have found a quite narrow distribution of hydrogen bonding energies from 1 to 8 kJ/mol with the average energy of intra-protein hydrogen bonds h¯=4.2±1.5 kJ/mol and the average energy of water–protein bonds as hps¯=3.8±1.5 kJ/mol. This is an important illustration of a tiny disbalance between the water–protein and intraprotein hydrogen bonds. Fitted values of the nucleation parameter σ belong to the range from 0.001 to 0.01, as expected. The reported method can be considered as complementary to the classical two-state approach and together with other parameters provides the protein–water and intraprotein H-bonding energies, not accessible within the two-state paradigm.

Soil desiccation in the context of vegetation restoration: A scientometric analysis

AbstractThis research aims to fill the gap in understanding the evolution of soil desiccation studies, focusing on its impact on sustainable crop production in China's Loess Plateau. The study explores trends, influential works, authors, journals, and emerging research areas within the field of soil desiccation. To achieve this, this study pioneers a comprehensive scientometric exploration of soil desiccation. The study analyzed 1952 publications on soil desiccation from January 2013 to December 2023, sourced from the Web of Science. Various co‐citation techniques such as author co‐citation analysis (ACA), document co‐citation analysis (DCA), journal co‐citation analysis (JCA), and keyword analysis are employed. Network development, visualization tools, and text‐mining methods are utilized to discern patterns and relationships within the dataset. Here, for the first time, nine distinct clusters were identified through DCA. The findings reveal the impactful emergence of significant clusters, such as the one focusing on the Loess Plateau, marking a significant advance in our understanding of soil desiccation. Multiple research frontiers or sub‐specialties emerge, including topics such as different vegetation types, the impact on grain yield, water use efficiency, growth, soil water content, hydraulic redistribution, drought, soil moisture, and modeling. This innovative scientometric review of soil desiccation outlines the current scientific and technological trends while identifying knowledge gaps. The findings are beneficial for researchers, graduate students, and professors interested in understanding research trajectories, pivotal publications, and influential scholars shaping this field.

Walking-induced particle resuspension in a commercial airliner cabin under different ventilation systems

The potential health risk posed by particle resuspension in the air of an airliner cabin is a concern for passengers. This study employed computational fluid dynamics (CFD) to analyze particle dispersion patterns under different ventilation systems, such as mixing ventilation (MV), underfloor air distribution (UFAD), and aisle displacement ventilation (ADV), within a twin-aisle cabin environment. To ensure the accuracy of the CFD model, the study validated the simulated air velocity distribution against experimental airflow patterns from a small-scale water model reported in existing literature. Additionally, the research included direct measurements of particle resuspension within the breathing zone of a full-scale, twin-aisle cabin mockup, which featured five rows of seats. These measurements were taken in response to the disturbance caused by a volunteer walking over an aviation carpet in the aisle. While the CFD simulation results generally aligned with the experimental data, some discrepancies were noted. Pinpointing the exact causes of these discrepancies proved challenging due to the numerous uncertainties and approximations inherent in the study. Nevertheless, the investigation revealed that the air in the upper region near the moving body was pushed forward, creating a strong airflow that enveloped the body. This dynamic resulted in the formation of a wake that lifted particles from the floor level to the upper cabin area. The study observed that particle concentration within the breathing zone increased in the direction of movement. The airflow patterns produced by the three ventilation systems were different. Despite the cabin's symmetrical design, some particles can still transfer from one side to the other, especially under the MV system. The peak particle concentration in the breathing zone was recorded at 20 s, after which it decreased to negligible levels by 120 s. Among the ventilation systems analyzed, the MV system exhibited the highest peak particle concentration, while the UFAD system showed the lowest peak. However, the UFAD system also presented the possibility of very high particle concentrations at certain seats.

Spatio-temporal variability of soil water content across plot scales within a vineyard

Understanding spatio-temporal variability of soil water content (SWC) at different scales is of great importance for designing monitoring networks and assimilating observed data in hydrological modeling. The objective of the study was to examine spatio-temporal variability of SWC for different soil layers at different extent scales within an agricultural field. Spatio-temporal variability of SWC and the relationship between variability and mean were investigated at three extent scales for different soil layers of 0–100 cm in different years within an intensively irrigated vineyard. Nested sampling grids were used, and at each scale, there was a total of 16 points distributed regularly at the grids. The distance between any two adjacent sampling points was 25-m, 50-m, and 75-m for the three scales respectively. Overall, there was no consistent pattern regarding the change of mean, standard deviation (SD), and coefficient of variation (CV) with scales during the three years. For the surface soil layer, mean SWC was similar between scales, while SD was closely related to soil clay content at the sampling locations of each scale. For subsurface soils, the overall magnitude of variability of SWC was greater, whereas the difference in the variability between scales was lower than that of the soil texture of the corresponding soil layer. The proportional decrease of CV with increasing mean was found to be largely consistent between different years for all soil layers excluding 20–40 cm, but variable between scales and soil layers. For subsurface soil layers, the CV vs. mean relationship differed between relatively wet and dry years, indicating that factors controlling SWC dynamics for the layers below the surface layer were different depending on climatic conditions. Variance partitioning analysis showed that spatial variance accounted for at least 57 % of total variance for all cases, and the temporal variance at different scales fluctuated within a narrow range for subsurface soils for the three years. The results could benefit soil water content monitoring network design, calibration of soil moisture related parameters and assimilation of observed soil moisture data into field soil water modeling.

Local-in-space wave breaking criteria for a generalized rod equation

A generalized rod equation including the celebrated Camassa–Holm shallow water model is considered. The blow-up features of the equation are discussed on the line R. Using the method to construct the Lyapunov functions, local-in-space wave breaking criteria to the equation are established. Our wave breaking results are only involved in the initial values V0(x0) and V0′(x0) at a single local point x0∈R.

Research on the water flooding front based on dynamic and static data inversion – a case study

To clarify the movement of the water flooding front in fluvial reservoirs, this research takes the BZ oilfield as an example. By considering the equivalent flow resistance theory for oil–water two-phase flow, the horizontal micro-element equivalent method and the strong heterogeneity of fluvial facies reservoir comprehensively, a calculation model for a non-piston water flooding front in a horizontal well pattern was established. First, five horizontal injection–production well groups in the BZ oilfield were taken as examples to calculate the water breakthrough time for the oil wells. The calculation results are in good agreement with the actual production performance. In detail, the advancing speed of the water flooding front in the high-permeability strip was 0.8–1.6 m/day, and the speed in the low-permeability strip was 0.12–0.35 m/day. When water is seen in the oil well, the advancing speed in the low-permeability strip is reduced, resulting in uneven displacement and the formation of non-dominant potential areas. In addition, the water flooding front advancing distance was simulated to be 300–450 m by establishing a reservoir numerical simulation model, which is close to the result of the proposed model, indicating that the calculation method is reliable. This research is of great significance for predicting the water breakthrough time of horizontal production wells, judging the weak affected area on the mainstream line, and optimizing water injection and tapping reservoir potential in good time.

Interrogating Explicit Solvent Effects on the Mechanism and Site-Selectivity of Aryl Halide Oxidative Addition to L2Pd(0).

We report a study of solvent effects on the rate, selectivity, and mechanism of (hetero)aryl (pseudo)halide oxidative addition to Pd(PCy3)2 as an exemplar of L2Pd(0) species. First, 2-chloro-3-aminopyridine is observed to undergo faster oxidative addition in toluene compared to more polar solvents, which is not consistent with the trend we observe with many other 2-halopyridines. We attribute this to solvent basicity hydrogen-bonding (pKHB) between solvent and substrate. Greater hydrogen-bond donation from the substrate leads to a more electron-rich aromatic system, and therefore slower oxidative addition. We demonstrate how this affects rate and site-selectivity for hydrogen-bond donating substrates. Second, electron-deficient multihalogenated pyridines exhibit improved site-selectivity in polar solvents, which we attribute to different C-X sites undergoing oxidative addition by two different mechanisms. The C-X site that favours the more polar nucleophilic displacement transition state is preferred over the site that favours a less-polar 3-centered transition state. Finally, (hetero)aryl triflates consistently undergo faster oxidative addition in more polar solvents, which we attribute to highly polar nucleophilic displacement transition states. This leads to improved site-selectivity for C-OTf oxidative addition, even in the presence of highly reactive 2-pyridylhalides.

Water model study on the mixing behaviour of gas-liquid two-phase flow for the SKS lead reduction process in a bottom-blown furnace

A 1:10.3 water model was constructed by geometrically scaling down an industrial bottom-blown furnace (BBF) used in the Shuikoushan (SKS) lead reduction process. An innovative method was devised, which combines a chemical decolorization technique with an image analysis method rooted in the RGB colour model, to visualize the mixing characteristics of gas–liquid two-phase flow and quantitatively assess fluid mixing time. The effects of various process parameters (the level height H, gas flow rate Q, feeding port P, vertical angle of the lance θ, and deflection angle of the lance relative to the wall normal α) on the mixing time t were studied via dimensional analysis. Furthermore, a mathematical correlation was developed for t as a function of Fr’, H/D (aspect ratio), P/D, θ, and α. Research findings can serve as a reference for the efficient smelting and optimal design of the SKS lead reduction process in a BBF.

Impact of north-west Bay of Bengal bathymetry along the off-coast of Digha on the propagation of shallow water waves using finite difference method

Numerical simulation of shallow water equations has been carried out using the Crank-Nicolson scheme of Finite Difference Method (FDM) to study the interaction of waves with different forms of bathymetry especially that of the off-coast of Digha, a tourist spot situated in the north-west coast of Bay of Bengal. MATLAB code has been developed for the simulation. One-dimensional (1-D) linear shallow water model has been considered here. Three different bathymetry profile are chosen for the investigation: (i) flat bathymetry (with or without seamount/basin); (ii) piecewise linear approximation to the real bathymetry of the off-coast of Digha; (iii) real bathymetry of the off-coast of Digha. Real bathymetry data has been obtained from the gridded data set of GEBCO (General Bathymetric Chart of the Oceans) published in 2022. Validation of the present numerical scheme has been performed by considering test problems with results existing in the literature. Comparative study of the effect of the bathymetries, on the propagation of shallow water waves, has been performed and demonstrated with figures and tables. Results of wave-bathymetry interaction obtained here are believed to be new with respect to the present study area and will definitely give some insight into the phenomena in this region.