Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank
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This paper presents a combination of models that together calculate the cage and roller speeds of a cylindrical roller bearing. The models consider elastohydrodynamic lubrication and contact elasticity between the roller and raceway, roller centrifugal forces, hydrodynamic lubrication at the cage pocket, and frictional forces. Using these models, the predicted cage and roller speeds and the extent of slip are compared to measurements acquired on cylindrical roller bearings in a commercial gearbox in steady-state and transient operating conditions of a wind turbine. In steady-state conditions at low wind speeds and low lubricant temperatures, cage and roller slip up to 60% occur in the loaded zone of the bearing. In the unloaded zone, up to 80% roller slip occurs. Cage and roller slip then decrease as the lubricant temperature and wind speed increases. In general, the analytical model results match experimental measurements within 10% for lubricant temperatures above 40 degrees C and wind speeds over 10 meters per second. The analytical model is further evaluated during a transient start-up event and highly dynamic emergency stop event and also used to examine changes in the bearing design or lubricant properties. Furthermore, roller and cage slip in cylindrical bearings is a combined effect of the bearing design, applied load, shaft speed, and lubricant properties and temperature, and can be quickly evaluated with the combined analytical models.
Dendritic cells are one of the most popular immune cells, which plays a remarkable role in both immunotherapy and tolerance induction. Due to unwanted side effects of leukocyte presence in donated blood, the policy of blood service is the pre-storage reduction of leukocytes, which today, filtration is the most common method for this purpose. The filtration method has led to diminished access to Buffy coat as a generally used conventional source of biological cells. We developed a simple, affordable, and reproducible method for dendritic cell differentiation from filter-derived monocytes and, the results of the filter study were compared with differentiated DCs from the conventional buffy coat-derived monocytes. The Monocytes were recovered from leukoreduction filter using an optimized protocol with supplemented PBS buffer. Following the adhesion method, CD14{sup +} Monocyte-enriched population with the purity of 94 % was obtained. After cytokine stimulation over a 6-day period and maturation induction by LPS, differentiated DCs were evaluated for morphology, surface markers (CD86, CD40, CD83 and, HLA-DR), antigen uptake potency and IL-12 secretion. Analysis and comparison of the results represented no significant difference between the two groups. Accordingly, we conclude that leukoreduction filters could be introduced as a reliable and research-grade source of monocyte for DC generation in biological research.
Recent theoretical progress using multiscale asymptotic analysis has revealed various possible regimes of stratified turbulence. Notably, buoyancy transport can either be dominated by advection or diffusion, depending on the effective Péclet number of the flow. Two types of asymptotic models have been proposed, which yield measurably different predictions for the characteristic vertical velocity and length scale of the turbulent eddies in both diffusive and non-diffusive regimes. The first, termed a ‘single-scale model’, is designed to describe flow structures having large horizontal and small vertical scales, while the second, termed a ‘multiscale model’, additionally incorporates flow features with small horizontal scales, and reduces to the single-scale model in their absence. By comparing predicted vertical velocity scaling laws with direct numerical simulation data, we show that the multiscale model correctly captures the properties of strongly stratified turbulence within regions dominated by small-scale isotropic motions, whose volume fraction decreases as the stratification increases. Meanwhile its single-scale reduction accurately describes the more orderly, layer-like, quiescent flow outside those regions.
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Due to the recent boom in shale gas production, aromatics production using direct nonoxidative methane dehydroaromatization (DHA) is being investigated extensively. However, due to rapid coke formation, catalysts in the nonoxidative methane DHA reactors get deactivated, which is one of the critical issues for the commercial success of the methane DHA process. In this paper, a model for catalyst deactivation is developed. Rate models for other DHA reactions are developed by considering the decrease in the catalyst activity with time. Due to the very fast coke formation rate on the fresh catalyst, there is coke formation immediately upon the introduction of the feed. Therefore, an algorithm is developed for estimation of the initial state of the reactor and the kinetic parameters by coupling an iterative direct substitution approach with an optimization approach. Transient experimental data from an in-house reactor are first reconciled and then used for developing the kinetic model including the coke formation model. Using the rate model, a dynamic, heterogeneous, multiscale reactor model with embedded heating is developed. Here, the model couples the catalyst pellet level model with a reactor level model. Impacts of temperature, L/D ratio, and scheduling of reactors on variability in conversion and yield with time are studied.
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Electronic structure calculations in enzymes converge very slowly with respect to the size of the model region that is described using quantum mechanics (QM), requiring hundreds of atoms to obtain converged results and exhibiting substantial sensitivity (at least in smaller models) to which amino acids are included in the QM region. As such, there is considerable interest in developing automated procedures to construct a QM model region based on well-defined criteria. However, testing such procedures is burdensome due to the cost of large-scale electronic structure calculations. Here, we show that semiempirical methods can be used as alternatives to density functional theory (DFT) to assess convergence in sequences of models generated by various automated protocols. The cost of these convergence tests is reduced even further by means of a many-body expansion. We use this approach to examine convergence (with respect to model size) of protein–ligand binding energies. Fragment-based semiempirical calculations afford well-converged interaction energies in a tiny fraction of the cost required for DFT calculations. Two-body interactions between the ligand and single-residue amino acid fragments afford a low-cost way to construct a “QM-informed” enzyme model of reduced size, furnishing an automatable active-site model-building procedure. This provides a streamlined, user-friendly approach for constructing ligand binding-site models that needs neither a priori information nor manual adjustments. Extension to model-building for thermochemical calculations should be straightforward.
Constrained density functional theory (CDFT) is a powerful tool for the prediction of electron transfer parameters in condensed phase simulations at a reasonable computational cost. In this work we present an extension to CDFT in the popular mixed Gaussian/plane wave electronic structure package CP2K, implementing the additional force terms arising from a constraint based on Hirshfeld charge partitioning. This improves upon the existing Becke partitioning scheme, which is prone to give unphysical atomic charges. We verify this implementation for a variety of systems: electron transfer in (H 2 O) 2 + in vacuum, electron tunnelling between oxygen vacancy centers in solid MgO, and electron self-exchange in aqueous Ru 2+ -Ru 3+ . We find good agreement with previous plane-wave CDFT results for the same systems, but at a significantly lower computational cost, and we discuss the general reliability of condensed phase CDFT calculations.
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Amines play several key roles in chemistry and biology and are involved in numerous industrial processes, often with significant economic impacts. Recently, amines are also garnering interest as catalysts for polymer synthesis and for CO 2 fixation, incentivizing the need to rapidly design and screen new amino compounds. Hence, developing reliable methods to predict their physicochemical properties, e.g., the base dissociation constant (pKb), is pivotal. Here, a density functional theory (DFT)-based approach was employed to compute the pKb of substituted amines, exploring the impact of several key parameters, including (i) the number of explicit water molecules at the reaction center, (ii) the van der Waals (vdW) surface, and (iii) solvent polarizability. In previous work, it was determined that including two explicit water molecules at the reaction center resulted in highly accurate pKb estimates for primary amines. Here, we find that including a third water molecule at the reaction center is essential for accurate pKb for secondary and tertiary amines. The revised methodology was then applied to a wider selection of amines, obtaining a minimum average error (MAE) < 0.4. In conclusion, this result represents an extension of our “easy-to-use method,” a simple and direct DFT approach exploiting CAM-B3LYP/SMD/6-311G+(d,p) to compute pKb without post facto modifications.
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