Viscoelastic models for Mexican heavy crude oil and comparison with a mixture of heptadecane and eicosane. Part I

The viscoelastic knowledge of crude oil is limited by the complexity and variability of the raw material. Viscoelastic models of Maxwell type describe widely Mexican crude oils when an Oldroyd contravariant derivative is considered. Moreover, a Weissenberg number is defined by the product of the shear rate and the characteristic time constituted by the inverse of the rate constant of C-C bonds rotations of alkanes. This dimensionless number allows the scaling of viscosities of both crude oil, at different temperatures, and mixtures of n-eicosane/n-heptadecane. Blends of linear alkanes can simulate the viscous behavior of crude oil after adequate scaling and can be used to predict crude oil rheological properties with the advantage to be completely known and reproducible systems.     

Electrical properties and phase of BaTiO3–SrTiO3 solid solution

It has been known that ABO₃ type perovskite ferroelectrics, such as BaTiO₃ (BTO) and SrTiO₃ (STO), form a complete solid solution. In this study, Ba_1?xSr_xTiO₃ (BST, x=0.0–1.0) solid solution were sintered by a solid-state reaction method using BTO and STO raw powders with appropriate chemical composition. The crystal structure was investigated by a Rietveld refinement method; Fullprof, using X-ray diffraction data. Within the reasonable goodness of fit, tetragonal symmetry was found in BST with x≤0.2, while BST with x≥0.4 were found to be cubic symmetry. However, Ba_0.7Sr_0.3TiO₃ was difficult to decide whether it is cubic or tetragonal because of large uncertainties after final fitting. The composition ratios calculated from the fitted occupancies match well with those measured by EDS within experimental uncertainties. Remnant polarizations of BST with x<0.3 decrease with increasing Sr concentration. Furthermore, measured phase transition temperatures and maximum dielectric constant decrease as increasing Sr concentration. Measured electrical properties of BST were match well with the structural refinement investigations.     

Thermal Motion and Conformational Disorder in Protein Crystal Structures: Comparison of Multi-Conformer and Time-Averaging Models

Models describing thermal motion and conformational variability in protein crystal structures were applied to the refinement of a 1.8 Å crystal structure of penicillopepsin. Three methods were tested: conventional refinement using restrained B factors, multiple-conformer refinement, and time-averaging refinement using molecular dynamics. The information content of the models was assessed by cross-validation and by estimating the phase accuracy of the model using phases obtained by multiple isomorphous replacement. The R value always decreased when using multi-conformer and time-averaging methods, as compared to conventional refinement. In contrast, the cross-validated (“free”) R value and the phase accuracy worsened for time-averaging in vacuum. Inclusion of solvent produced a slight improvement of both measures compared to conventional refinement. Multi-conformer refinements always improved both measures. An optimum was reached for simultaneous refinement of between four and eight conformers. At the resolution limit of the penicillopepsin data, multi-conformer refinement is an efficient method to describe conformational variability and thermal motion.     

Toward Real Real-Space Refinement of Atomic Models

High-quality atomic models providing structural information are the results of their refinement versus diffraction data (reciprocal-space refinement), or versus experimental or experimentally based maps (real-space refinement). A proper real-space refinement can be achieved by comparing such a map with a map calculated from the atomic model. Similar to density distributions, the maps of a limited and even inhomogeneous resolution can also be calculated as sums of terms, known as atomic images, which are three-dimensional peaky functions surrounded by Fourier ripples. These atomic images and, consequently, the maps for the respective models, can be expressed analytically as functions of coordinates, atomic displacement parameters, and the local resolution. This work discusses the practical feasibility of such calculation for the real-space refinement of macromolecular atomic models.     

A new framework for solution of multidimensional population balance equations

A new framework is proposed in this work to solve multidimensional population balance equations (PBEs) using the method of discretization. A continuous PBE is considered as a statement of evolution of one evolving property of particles and conservation of their n internal attributes. Discretization must therefore preserve n+1 properties of particles. Continuously distributed population is represented on discrete fixed pivots as in the fixed pivot technique of Kumar and Ramkrishna [1996a. On the solution of population balance equation by discretization—I. A fixed pivot technique. Chemical Engineering Science 51(8), 1311-1332] for 1-d PBEs, but instead of the earlier extensions of this technique proposed in the literature which preserve 2ⁿ properties of non-pivot particles, the new framework requires n+1 properties to be preserved. This opens up the use of triangular and tetrahedral elements to solve 2-d and 3-d PBEs, instead of the rectangles and cuboids that are suggested in the literature. Capabilities of computational fluid dynamics and other packages available for generating complex meshes can also be harnessed. The numerical results obtained indeed show the effectiveness of the new framework. It also brings out the hitherto unknown role of directionality of the grid in controlling the accuracy of the numerical solution of multidimensional PBEs. The numerical results obtained show that the quality of the numerical solution can be improved significantly just by altering the directionality of the grid, which does not require any increase in the number of points, or any refinement of the grid, or even redistribution of pivots in space. Directionality of a grid can be altered simply by regrouping of pivots.     

Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy

Protein structure refinement is a crucial step for more accurate protein structure predictions. Most existing approaches treat it as an energy minimization problem to intuitively improve the quality of initial models by searching for structures with lower energy. Considering that a single energy function could not reflect the accurate energy landscape of all the proteins, our previous AIR 1.0 pipeline uses multiple energy functions to realize a multi-objectives particle swarm optimization-based model refinement. It is expected to provide a general balanced conformation search protocol guided from different energy evaluations. However, AIR 1.0 solves the multi-objective optimization problem as a whole, which could not result in good solution diversity and convergence on some targets. In this study, we report a decomposition-based method AIR 2.0, which is an updated version of AIR, for protein structure refinement. AIR 2.0 decomposes a multi-objective optimization problem into a number of subproblems and optimizes them simultaneously using particle swarm optimization algorithm. The solutions yielded by AIR 2.0 show better convergence and diversity compared to its previous version, which increases the possibilities of digging out better structure conformations. The experimental results on CASP13 refinement benchmark targets and blind tests in CASP 14 demonstrate the efficacy of AIR 2.0.     

Analytical solution for electrolyte concentration distribution in lithium-ion batteries

In this article, the method of separation of variables (SOV), as illustrated by Subramanian and White (J Power Sources 96:385, 2001), is applied to determine the concentration variations at any point within a three region simplified lithium-ion cell sandwich, undergoing constant current discharge. The primary objective is to obtain an analytical solution that accounts for transient diffusion inside the cell sandwich. The present work involves the application of the SOV method to each region (cathode, separator, and anode) of the lithium-ion cell. This approach can be used as the basis for developing analytical solutions for battery models of greater complexity. This is illustrated here for a case in which non-linear diffusion is considered, but will be extended to full-order nonlinear pseudo-2D models in later work. The analytical expressions are derived in terms of the relevant system parameters. The system considered for this study has LiCoO₂–LiC₆ battery chemistry.     

Optimality-based grid adaptation for input-affine optimal control problems

This paper studies the solution accuracy of direct single-shooting in comparison to the solution of the continuous optimal control problem (OCP). First, a convergence relation between the solution of the nonlinear program and that of continuous OCP is analyzed by means of an exemplary problem. This example reveals that Pontryagin's minimum principle cannot be used as a stopping criterion for optimality-based control grid adaptation. Consequently, a novel grid refinement strategy is introduced, which is rather based on the switching function and thus limited to the class of input-affine OCPs. Grid points are eliminated and inserted such that the approximation of the optimality condition of the OCP, elucidated by the switching function, is improved. The suggested methodology is illustrated and compared to a previously published wavelet-based adaptation approach by means of two reactor optimization problems with different solution characteristics.     

Analytical models of adhesively bonded joints—Part I: Literature survey

An extensive literature review on existing analytical models for both single and double-lap joints has been made to assist the designer to choose the right model for a particular application. The literature review shows that almost all analytical models for adhesively bonded lap joints are two-dimensional. This is generally sufficient because the stresses in the width direction are significantly lower than in the direction of the loading. Most of the analyses are linear elastic for both adherends and adhesive because the inclusion of material non-linearity renders the solution too complex. As the degree of complexity and the number of stress components in the adhesive and the adherends increase, the initial analytical problem must be solved numerically. A summary of the main analyses is presented indicating the conditions of applicability and the stress components considered. A comparative study of various models of increasing complexity and how strength predictions based on these models compare with experimental data is presented in an accompanying paper.     

Enhanced tribological properties of MWCNT/Ni bulk composites – Influence of processing on friction and wear behaviour

The friction and wear behaviour of MWCNT-reinforced Ni matrix bulk composites is investigated and compared to the response of a pure bulk reference sample. Several effects are observed in the composites such as microstructural refinement, leading to improved hardness, coefficient of friction and wear resistance. Said refinement might also be responsible for a non-trivial behaviour of hot-pressed composites under a 300 mN load, due to higher oxidation rates. The worn volume is analysed and discussed from a microstructural and morphological point of view. In this context, a direct correlation is shown between two relevant wear parameters, namely, the wear constant K and the cutting efficiency f_AB. In addition, the tribochemistry is investigated by Raman spectroscopy and linked to the friction and wear behaviour. Finally, the wear volume reduction peaked at 94.1% in HUP samples. This clearly indicates the high potential of these composites for tribological applications.     

Use of dynamically adaptive grid techniques for the solution of electrochemical kinetic equations: Part 16: Patch-adaptive strategy combined with the extended Numerov spatial discretisation

Electrochemical kinetic simulations by the patch-adaptive strategy outlined in the previous parts of this series of papers can be computationally expensive in the extreme cases of very thin boundary layers, moving fronts, or models defined over multiple spatial subintervals having disparate scales. The replacement of the second-order accurate conventional spatial discretisation (thus far used by the strategy) by the fourth-order accurate extended Numerov discretisation of Chawla [M.M. Chawla, J. Inst. Math. Appl. 22 (1978) 89], discussed in this work, allows one to reduce the computational costs. Numerical experiments with five representative examples of difficult-to-simulate kinetic models reveal that the reduction of the computational time, the number of spatial grid nodes needed, and spatial grid refinement levels, is particularly noticeable when a high spatial accuracy of the simulations is requested. At low accuracy demands the conventional spatial discretisation may be more efficient and more convenient to use. The patch-adaptive simulations by the extended Numerov scheme require spatial tolerance parameter TOLX values that are several times larger than the TOLX values that ensure a comparable accuracy by the conventional spatial discretisation.     

Mass transfer enhancement in the Membrane Aromatic Recovery System (MARS): theoretical analysis

This work investigates three different models describing mass transfer enhancement by a reversible and instantaneous second-order chemical reaction. The three models are applied to the study of mass transfer phenomena occurring in a membrane process for recovery of organic chemicals, the Membrane Aromatic Recovery System (MARS). Typical MARS operating conditions are used as model inputs, and the results obtained are used to assess the degree of complexity that should be taken into account in describing the mass transfer phenomena. The most complex model derived (N-P model) accounts for chemical reaction reversibility and the Nernst-Planck effect created by ionic species and is solved numerically. Following Olander model for a second order reversible instantaneous reaction model is proposed, for which we derive an analytical solution in terms of bulk solution properties. Finally, the simplest model follows the analysis of Hatta, assuming irreversible chemical reaction and neglecting the Nernst-Planck effect. The reversibility of the reaction is shown to be important, while N-P effects are negligible. The Olander model is recommended for use in describing the mass transfer phenomena. The models developed can be applied further to other processes of similar type.     

Dynamic simulation of a 2D bubble column

The present paper demonstrates how 2D, dynamic simulations of a flat bubble column are feasible, applying state-of-the-art dynamic turbulence models, when an appropriate turbulent dispersion term is applied in the conservation equation for the gas volume fraction. The kω turbulence model yielded a better qualitative prediction of the bubble plume than the kε model, due to the low-Reynolds number treatment of the former model. The simple mixing length turbulence model gave the best prediction of the meandering plume, without any dispersion term. The mixing length model is, however, almost identical to a Large-Eddy simulation when run time-dependent on a fine mesh, and should be applied with care due to the use of a constant turbulence length scale and the inherent 3D nature of turbulence. By refining the mesh to the extreme end, it was shown that an apparently grid independent numerical solution was really grid-dependent, even when dynamic turbulence models were applied. The apparently grid independent solution was computed with an increment in the computational mesh that was of the same size as an equilibrium Kolmogorov length scale.     

A Systems Biology Approach to Understanding the Mechanisms of Action of Chinese Herbs for Treatment of Cardiovascular Disease

Traditional Chinese Medicine (TCM) involves a broad range of empirical testing and refinement and plays an important role in the health maintenance for people all over the world. However, due to the complexity of Chinese herbs, a full understanding of TCM’s action mechanisms is still unavailable despite plenty of successful applications of TCM in the treatment of various diseases, including especially cardiovascular diseases (CVD), one of the leading causes of death. Thus in the present work, by incorporating the chemical predictors, target predictors and network construction approaches, an integrated system of TCM has been constructed to systematically uncover the underlying action mechanisms of TCM. From three representative Chinese herbs, i.e., Ligusticum chuanxiong Hort., Dalbergia odorifera T. Chen and Corydalis yanhusuo WT Wang which have been widely used in CVD treatment, by combinational use of drug absorption, distribution, metabolism and excretion (ADME) screening and network pharmacology techniques, we have generated 64 bioactive ingredients and identified 54 protein targets closely associated with CVD, of which 29 are common targets (52.7%) of the three herbs. The result provides new information on the efficiency of the Chinese herbs for the treatment of CVD and also explains one of the basic theories of TCM, i.e., “multiple herbal drugs can treat one disease”. The predicted potential targets were then mapped to target-disease and target-signal pathway connections, which revealed the relationships of the active ingredients with their potential targets, diseases and signal systems. This means that for the first time, the action mechanism of these three important Chinese herbs for the treatment of CVD is uncovered, by generating and identifying both their active ingredients and novel targets specifically related to CVD, which clarifies some of the common conceptions in TCM, and thus provides clues to modernize such specific herbal medicines.     

Influence of particle size on magnetic and electromagnetic properties of hexaferrite synthesised by sol-gel auto combustion route

Magnetoplumbite barium hexaferrite (BaFe_11.8Co_0.2O₁₉) is synthesised through sol-gel auto-combustion method under two pH conditions of precursor solutions (acidic i.e. pH < 1 and neutral i.e. pH = 7). The XRD analysis followed by Reitveld refinement indicates the formation of phase pure samples in both cases but the barium hexaferrite obtained from acidic precursor solution has smaller crystallite sizes. The Transmission Electron Microscopy (TEM) analysis followed by High Resolution Transmission Electron Microscopy (HRTEM) confirms a lower particle size of ～20 nm for barium hexaferrite synthesised from acidic pH precursor solution. The shift in Raman peak (520-540 cm^?1) by 20 cm^?1, represents the whole structural block and further confirms the differences in the distribution of particle sizes due to the method of synthesis. The magnetic studies display a lower coercive field for the samples with smaller particle sizes. This is due to the crystalline size-induced microstrain that controls the magneto-crystalline anisotropy, shape anisotropy and stress anisotropy. The electromagnetic characterisation confirms broader absorption in the range of 8–18 GHz (X-band) with R_L ≤ ?7 db for the entire range for the samples with smaller particle sizes.     

Torsional random walk statistics on lattices using convolution on crystallographic motion groups

This paper presents a new algorithm for generating the conformational statistics of lattice polymer models. The inputs to the algorithm are the distributions of poses (positions and orientations) of reference frames attached to sequentially proximal bonds in the chain as it undergoes all possible torsional motions in the lattice. If z denotes the number of discrete torsional motions allowable around each of the n bonds, our method generates the probability distribution in end-to-end pose corresponding to all of the zⁿ independent lattice conformations in O(n^D+1) arithmetic operations for lattices in D-dimensional space. This is achieved by dividing the chain into short segments and performing multiple generalized convolutions of the pose distribution functions for each segment. The convolution is performed with respect to the crystallographic space group for the lattice on which the chain is defined. The formulation is modified to include the effects of obstacles (excluded volumes) and to calculate the frequency of the occurrence of each conformation when the effects of pairwise conformational energy are included. In the latter case (which is for three dimensional lattices only) the computational cost is O(z⁴n⁴). This polynomial complexity is a vast improvement over the O(zⁿ) exponential complexity associated with the brute-force enumeration of all conformations. The distribution of end-to-end distances and average radius of gyration are calculated easily once the pose distribution for the full chain is found. The method is demonstrated with square, hexagonal, cubic and tetrahedral lattices.     

A novel free boundary algorithm for the solution of cell population balance models

There exists an abundance of experimental evidence in a variety of systems, showing that cell populations are heterogeneous systems in the sense that properties such as size, shape, DNA and RNA content are unevenly distributed amongst the cells of the population. The quantitative understanding of heterogeneity is of great significance, since neglecting its effect can lead to false predictions. Cell population balance models are used to address the implications of heterogeneity and can accurately capture the dynamics of heterogeneous cell populations. They are first-order partial-integral differential equations and due to the complexity of formulation, analytical solutions are hard to obtain in the majority of cases. Despite the recent progress, the efficient solution of cell population balance models remains a challenging task. One of the main challenges stems from the fact that the boundaries of the intracellular state space are typically not known a priori and using fixed-boundary algorithms leads to inaccuracies and increased computational time demands. Motivated by this challenge, we formulated a free boundary finite element algorithm, capable of solving cell population balance equations more efficiently than the traditional fixed-boundary algorithms. The implementation of the algorithm is accommodated, in the finite element based software package COMSOL Multiphysics. We demonstrate the efficiency of this algorithm using the lac operon gene regulatory network as our model system and perform transient and asymptotic behavior analysis. In the latter case, the pseudo-arc-length continuation algorithm is incorporated, in order to investigate the existence of a bistability region, also observed at the single-cell level. Our analysis, revealed the existence of a region of bistability when cell heterogeneity is taken into account; however, its extend shrinks comparing to homogeneous cell populations. The free boundary algorithm can be easily extended for problems of higher dimensionality and we present results for a two-dimensional cell population balance model, which can exhibit an oscillatory behavior. It is shown that oscillations do not persist when the intracellular content is unevenly distributed amongst the daughter cells.     

Investigation on the structural and microstructural properties of copper-doped hydroxyapatite coatings deposited using solution precursor plasma spraying

Structural and microstructural investigation of solution precursor plasma sprayed copper-doped hydroxyapatite coatings with different Cu dopant concentration was carried out. Scanning electron micrographs did not show any significant morphological changes at the surface and cross-section of the coatings as copper content increases. X-ray diffraction results showed the decrease in the HA phase content from 93 wt.% to 14 wt.% and its degree of crystallinity from 94% to 85% with increasing copper concentration. Raman and IR spectra revealed the broadening and red-shifting of the phosphate bands due to the distortion of the HA structure caused by possible insertion of copper. X-ray photoelectron spectroscopy identified Cu and Cu²⁺ as copper species incorporated in HA. Rietveld refinement showed an increase in the lattice a and c parameter and expansion of the unit cell volume associated to an interstitial insertion of Cu along the hexagonal channel of the HA structure.     

PCD Genes—From Patients to Model Organisms and Back to Humans

Primary ciliary dyskinesia (PCD) is a hereditary genetic disorder caused by the lack of motile cilia or the assembxly of dysfunctional ones. This rare human disease affects 1 out of 10,000–20,000 individuals and is caused by mutations in at least 50 genes. The past twenty years brought significant progress in the identification of PCD-causative genes and in our understanding of the connections between causative mutations and ciliary defects observed in affected individuals. These scientific advances have been achieved, among others, due to the extensive motile cilia-related research conducted using several model organisms, ranging from protists to mammals. These are unicellular organisms such as the green alga Chlamydomonas, the parasitic protist Trypanosoma, and free-living ciliates, Tetrahymena and Paramecium, the invertebrate Schmidtea, and vertebrates such as zebrafish, Xenopus, and mouse. Establishing such evolutionarily distant experimental models with different levels of cell or body complexity was possible because both basic motile cilia ultrastructure and protein composition are highly conserved throughout evolution. Here, we characterize model organisms commonly used to study PCD-related genes, highlight their pros and cons, and summarize experimental data collected using these models.