A database of calculated solution parameters for the recently released AlphaFold predicted protein structures

Recent spectacular advances by AI programs in 3D structure predictions from protein sequences have revolutionized the field in terms of accuracy and speed. The resulting "folding frenzy" has already produced predicted protein structure databases for the entire human and other organisms' proteomes. However, rapidly ascertaining a predicted structure's reliability based on measured properties in solution should be considered. Shape-sensitive hydrodynamic parameters such as the diffusion and sedimentation coefficients (D0t(20,w),s0(20,w)) and the intrinsic viscosity ([η]) can provide a rapid assessment of the overall structure likeliness, and SAXS would yield the structure-related pair-wise distance distribution function p(r) vs. r. Using the extensively validated UltraScan SOlution MOdeler (US-SOMO) suite we have calculated from the AlphaFold structures the corresponding D0t(20,w), s0(20,w), [η], p(r) vs. r, and other parameters. Circular dichroism spectra were also computed. The resulting US-SOMO-AF database should aid in rapidly evaluating the consistency in solution of AlphaFold predicted protein structures.

Identification of particular hydrodynamic parameters for a modular type 4 DOF underwater vehicle by means of CFD method

Purpose The development of robust control algorithms for the position, velocity and trajectory control of unmanned underwater vehicles (UUVs) depends on the accuracy of their mathematical models. Accuracy of the model is determined by precise estimation of the UUV hydrodynamic parameters. The purpose of this study is to determine the hydrodynamic forces and moments acting on an underwater vehicle with complex body geometry and moving at low speeds and to achieve the accurate coefficients associated with them. Design/methodology/approach A three-dimensional (3D) computer-aided design (CAD) model of UUV is designed with one-to-one dimensions. 3D fluid flow simulations are conducted using computational fluid dynamics (CFD) software programme in the solution of Navier Stokes equations for laminar and turbulent flow analysis. The coefficients depending on the hydrodynamic forces and moments are determined by the external flow analysis using the CFD programme. The Flow Simulation k-ε turbulence model is used for the transition from laminar flow to turbulent flow. Hydrodynamic properties such as lift and drag coefficients and roll and yaw moment coefficients are calculated. The parameters are compared with the coefficient values found by experimental methods. Findings Although the modular type UUV has a complex body geometry, the comparative results of the experiments and simulations confirm that the defined model parameters are accurate and close to the actual experimental values. In the proposed k-ε method, the percentage error in the estimation of drag and lifting coefficients is decreased to 4.2% and 8.39%, respectively. Practical implications The model coefficients determined in this study can be used in high-level control simulations which leads to the development of robust real-time controllers for complex-shaped modular UUVs. Originality/value The Lucky Fin UUV with 4 degrees of freedom is a specific design and its CAD model is first extracted. Verification of simulation results by experiments is generally less referenced in studies. However, it provides more precise parameter identification of the model. Proposed study offers a simple and low-cost experimental measurement method for verification of the hydrodynamic parameters. The extracted model and coefficients are worthwhile references for the analysis of modular type UUVs.

New Insights from Locally Resolved Hydrodynamics in Stirred Cell Culture Reactors

The link between hydrodynamics and biological process behavior of antibody-producing mammalian cell cultures is still not fully understood. Common methods to describe dependencies refer mostly to averaged hydrodynamic parameters obtained for individual cultivation systems. In this study, cellular effects and locally resolved hydrodynamics were investigated for impellers with different spatial hydrodynamics. Therefore, the hydrodynamics, mainly flow velocity, shear rate and power input, in a single- and a three-impeller bioreactor setup were analyzed by means of CFD simulations, and cultivation experiments with antibody-producing Chinese hamster ovary (CHO) cells were performed at various agitation rates in both reactor setups. Within the three-impeller bioreactor setup, cells could be cultivated successfully at much higher agitation rates as in the single-impeller bioreactor, probably due to a more uniform flow pattern. It could be shown that this different behavior cannot be linked to parameters commonly used to describe shear effects on cells such as the mean energy dissipation rate or the Kolmogorov length scale, even if this concept is extended by locally resolved hydrodynamic parameters. Alternatively, the hydrodynamic heterogeneity was statistically quantified by means of variance coefficients of the hydrodynamic parameters fluid velocity, shear rate, and energy dissipation rate. The calculated variance coefficients of all hydrodynamic parameters were higher in the setup with three impellers than in the single impeller setup, which might explain the rather stable process behavior in multiple impeller systems due to the reduced hydrodynamic heterogeneity. Such comprehensive insights lead to a deeper understanding of the bioprocess.

Numerical simulation of groundwater in an unconfined aquifer with a novel hybrid model (case study: Birjand Aquifer, Iran)

In recent decades, due to the population growth and low precipitation, the overexploitation of ground water resources has become an important issue. To ensure a sustainable scheme for these resources, understanding the behavior of the aquifers is a key step. This study takes a numerical modeling approach to investigate the behavior of an unconfined aquifer in an arid area located in the east of Iran. A novel hybrid model is proposed that couples the numerical modeling to a data assimilation model to remove the uncertainty in the hydrodynamic parameters of the aquifer including the hydraulic conductivity coefficients and specific yields. The uncertainty that exists in these parameters results in unreliability of the head values acquired from the models. Meshless local Petrov-Galerkin (MLPG) is used as the numerical model, and particle filter (PF) is our data assimilation model. These models are implemented in the MATLAB software. We have calibrated and validated our PF-MLPG model by the observation head data from the piezometers. The RMSE in head values for our model and other commonly used numerical models in the literature including the finite difference method and MPLG are calculated as 0.166, 1.197 and 0.757 m, respectively. This fact shows the necessity of using this method in each aquifer.

A STUDY ON SUDDEN EXPANSION HYDRODYNAMIC PHENOMENA OCCURRING IN CYLINDRICAL PIPES

Introduction: This paper studies the frequency with which hydrodynamic parameters change in the sudden expansion section of axisymmetric pressure flow, based on the boundary layer equations. Methods: The suggested method reveals the regularity of changes in the hydrodynamic parameters of the flow in the transitional area, making it possible to obtain a velocity profile in any cross-section under common initial and boundary conditions. Based on the general solutions, we studied the hydrodynamic processes occurring in the transitional area of the effective sudden cross-section expansion within the axisymmetric pressure movement, in the following cases: a) when the velocity is constant at any point of the inlet face; b) when the velocity is distributed along the inlet face according to the parabolic law. Our calculations were carried out for different values of the expansion factor. Results: Based on the results of the computer-aided experimental study, we obtained velocity diagrams along the length of the transitional area with constant and parabolic velocity distributions for fluid inflowing into the expanded section. We also determined the patterns of pressure distribution along the length of the relevant section.

Evidence of Microplastic Size Impact on Mobility and Transport in the Marine Environment: A Review and Synthesis of Recent Research

Marine Microplastics (MPs) exhibit a wide range of properties due to their variable origins and the weathering processes to which they are exposed. MP’s versatile properties are connected to their dispersal, accumulation, and deposition in the marine environment. MP transport and dispersion are often explained by analogy with sediments. For natural sediments, one of the key features linked to transport and marine morphology is particle size. There is, however, no size classification defined for MP particles and MPs constitute all plastic particles sized smaller than the threshold of 5 mm. In this study, based on existing knowledge in hydrodynamics and natural sediment transport, the impact of MP size on turbulent entrainment, particle settling, and resuspension is described. Moreover, by analyzing several quantitative studies that have provided size distribution, size-selective accumulation of MPs in various regions of the marine environment is reported on. The preferential presence of MPs based on their size in different marine compartments is discussed based on the governing hydrodynamic parameters. Furthermore, the linkage between polymer properties and MP shape and size is explored. Despite the evident connection between hydrodynamic transport and MP size presented, classification of MP size presents challenges. MP size, shape, and density appear simultaneously in the definition of many hydrodynamic parameters described in this study. Unlike mineral sediments that possess a narrow range of density and shape, plastics are manufactured in a wide variety of densities and marine MPs are versatile in shape. Classification for MP size should incorporate particle variability in terms of polymer density and shape.

Estimation of the Hydrodynamic Parameters of Soils Subjected to Water Scarcity: Application of BEST and Introduction of a Specific Methodology

Propose a specific method (Junction Between Arya and Heitman and Haverkamp - JAHH), similar to BEST, to obtain the hydrodynamic parameters of soils in Pernambuco, Brazil. Sample: Department of Civil Engineering, Polytechnic School of Pernambuco – POLI, between March 2019 and February 2021. For this, BEST and JAHH were used to obtain the hydrodynamic characteristics of the collected materials, and the results of both methods were compared with simulations performed in Hydrus-1D. Sorptivity and Ks, acquired using both methods, presented differences reached 68.38% regarding Ks. The characteristic radius of the pores (λm) and capillary length (λc) obtained with BEST are not coherent, and this can be explained because during the evaluation of one sandy soil, λm values were the highest and λc were the lowest, when the opposite was expected. The use of JAHH to estimate soil parameters could generate more coherent estimates than BEST-slope, even though both of them have presented results of the same proportion, such as sorptivity and saturated hydraulic conductivity, for exemple. Therefore, the proposed method presented more pertinent results when compared to BEST regarding the studied soils.

Determination of the Hydrodynamic Parameters of Two Types of Soil in the Senegal River Delta. Simulation of Hydro-saline Transfers: Application to the Wind Deflation Phenomenon

In the Senegal River delta, the presence of a shallow salt water table associated with a strong evaporative demand sometimes leads to an upwelling of salts that crystallize on the surface. This phenomenon can be observed in the vicinity of the Diawling Basin, where a powdery structure sensitive to wind deflation and a massive structure with a fractionation into platelets that cannot be transported by the wind are noted. To understand the hydrodynamic characteristics of these soils, we used numerical simulation of water and solute transfers. The hydrodynamic parameters were determined in the laboratory using Wind's method on undisturbed samples. The experimental retention h() and hydraulic conductivity K(h) curves were fitted using the Van Genuchten model. The simulations show that the soil with a powdery structure has hydrodynamic characteristics that favour the ascent of salts from the water table to the surface. For the soil with a massive structure, the hydrodynamic conditions impose a deposition of salts in the subsurface.

Individual Fracture Efficiency Monitoring in Horizontal Wells by Using a New 3d Fine-Grid Temperature Modelling

Profitable development of hard-to-recover reserves often involves drilling of horizontal wells with multistage hydraulic fracturing to increase the oil recovery factor. Usually to monitor the fracture sweep efficiency, pressure transient analysis is used. However, in case of several fractures this method delivers only average hydrodynamic parameters of the well-fracture system. This paper illustrates the value of temperature logging data and demonstrates possibilities of the 3-D thermo-mechanical modelling in evaluating the differential efficiency of multi-stage hydraulic fracturing.