Two-scale computational modelling of unsaturated flow in soils exhibiting small scale heterogeneities

Unsaturated water flow in soil is commonly modelled using Richards’ equation, which requires the hydraulic properties of the soil (e.g., porosity, hydraulic conductivity, etc.) to be characterised. Naturally occurring soils, however, are heterogeneous in nature, that is, they are composed of a number of interwoven homogeneous soils each with their own set of hydraulic properties. When the length scale of these soil heterogeneities is small, numerical solution of Richards’ equation is computationally impractical due to the immense effort and refinement required to mesh the actual heterogeneous geometry. A classic way forward is to use a macroscopic model, where the heterogeneous medium is replaced with a fictitious homogeneous medium, which attempts to give the average flow behaviour at the macroscopic scale (i.e., at a scale much larger than the scale of the heterogeneities). Using the homogenisation theory, a macroscopic equation can be derived that takes the form of Richards’ equation with effective parameters. A disadvantage of the macroscopic approach, however, is that it fails in cases when the assumption of local equilibrium does not hold. This limitation has seen the introduction of two-scale models that include at each point in the macroscopic domain an additional flow equation at the scale of the heterogeneities (microscopic scale). This report outlines a well-known two-scale model and contributes to the literature a number of important advances in its numerical implementation. These include the use of an unstructured control volume finite element method and image-based meshing techniques, that allow for irregular micro-scale geometries to be treated, and the use of an exponential time integration scheme that permits both scales to be resolved simultaneously in a completely coupled manner. Numerical comparisons against a classical macroscopic model confirm that only the two-scale model correctly captures the important features of the flow for a range of parameter values.

Analysis of strain-rate dependent mechanical behavior of single chondrocyte : a finite element study

Various studies have been conducted to investigate the effects of impact loading on cartilage damage and chondrocyte death. These have shown that the rate and magnitude of the applied strain significantly influence chondrocyte death, and that cell death occurred mostly in the superficial zone of cartilage suggesting the need to further understand the fundamental mechanisms underlying the chondrocytes death induced at certain levels of strain-rate. To date there is no comprehensive study providing insight on this phenomenon. The aim of this study is to examine the strain-rate dependent behavior of a single chondrocyte using a computational approach based on Finite Element Method (FEM). An FEM model was developed using various mechanical models, which were Standard Neo-Hookean Solid (SnHS), porohyperelastic (PHE) and poroviscohyperelastic (PVHE) to simulate Atomic Force Microscopy (AFM) experiments of chondrocyte. The PVHE showed, it can capture both relaxation and loading rate dependent behaviors of chondrocytes, accurately compared to other models.

The effects of flexible fixation on early stage bone fracture healing

The mechanical microenvironment at a fracture site could potentially influence the outcomes of bone fracture healing. It is known that, should the fixation construct be too stiff, or the gap between the fracture ends be too large, bones are less likely to heal. Flexible fixation or so-called “biological fixation” has been shown to encourage the formation of fracture callus, and therefore result in better healing outcomes. However, till date the nature of the relationship between the degree of mechanical stability provided by a flexible fixation and optimal healing fracture healing outcomes has not been fully understood. This paper presents a computational model that can predict healing out-comes from early stage healing data under various fixation configurations. The results of the simulations demonstrate that the change of mechanical microenvironment of fracture site resulting from the different fixation configurations is of importance for the healing outcomes.

Validation tool for traction force microscopy

Traction force microscopy (TFM) is commonly used to estimate cells’ traction forces from the deformation that they cause on their substrate. The accuracy of TFM highly depends on the computational methods used to measure the deformation of the substrate and estimate the forces, and also on the specifics of the experimental set-up. Computer simulations can be used to evaluate the effect of both the computational methods and the experimental set-up without the need to perform numerous experiments. Here, we present one such TFM simulator that addresses several limitations of the existing ones. As a proof of principle, we recreate a TFM experimental set-up, and apply a classic 2D TFM algorithm to recover the forces. In summary, our simulator provides a valuable tool to study the performance, refine experimentally, and guide the extraction of biological conclusions from TFM experiments.

Computer simulation of scaffold degradation

Scaffolds are porous biocompatible materials with suitable microarchitectures that are designed to allow for cell adhesion, growth and proliferation. They are used in combination with cells in regenerative medicine to promote tissue regeneration by means of a controlled deposition of natural extracellular matrix by the hosted cells therein. This healing process is in many cases accompanied by scaffold degradation up to its total disappearance when the scaffold is made of a biodegradable material. This work presents a computational model that simulates the degradation of scaffolds. The model works with three-dimensional microstructures, which have been previously discretised into small cubic homogeneous elements, called voxels. The model simulates the evolution of the degradation of the scaffold using a Monte Carlo algorithm, which takes into account the curvature of the surface of the fibres. The simulation results obtained in this study are in good agreement with empirical degradation measurements performed by mass loss on scaffolds after exposure to an etching alkaline solution.

Computational aspects of probabilistic assessment of UAS robust autonomy

As the level of autonomy in Unmanned Aircraft Systems (UAS) increases, there is an imperative need for developing methods to assess robust autonomy. This paper focuses on the computations that lead to a set of measures of robust autonomy. These measures are the probabilities that selected performance indices related to the mission requirements and airframe capabilities remain within regions of acceptable performance.

Numerical investigation of mechanical and thermal dynamic properties of the industrial transformer

Industrial transformer is one of the most critical assets in the power and heavy industry. Failures of transformers can cause enormous losses. The poor joints of the electrical circuit on transformers can cause overheating and results in stress concentration on the structure which is the major cause of catastrophic failure. Few researches have been focused on the mechanical properties of industrial transformers under overheating thermal conditions. In this paper, both mechanical and thermal properties of industrial transformers are jointly investigated using Finite Element Analysis (FEA). Dynamic response analysis is conducted on a modified transformer FEA model, and the computational results are compared with experimental results from literature to validate this simulation model. Based on the FEA model, thermal stress is calculated under different temperature conditions. These analysis results can provide insights to the understanding of the failure of transformers due to overheating, therefore are significant to assess winding fault, especially to the manufacturing and maintenance of large transformers.

A meshfree-based local Galerkin method with condensation of degree of freedom for elastic dynamic analysis

Condensation technique of degree of freedom is first proposed to improve the computational efficiency of meshfree method with Galerkin weak form for elastic dynamic analysis. In the present method, scattered nodes without connectivity are divided into several subsets by cells with arbitrary shape. Local discrete equation is established over each cell by using moving Kriging interpolation, in which the nodes that located in the cell are used for approximation. Then local discrete equations can be simplified by condensation of degree of freedom, which transfers equations of inner nodes to equations of boundary nodes based on cells. The global dynamic system equations are obtained by assembling all local discrete equations and are solved by using the standard implicit Newmark’s time integration scheme. In the scheme of present method, the calculation of each cell is carried out by meshfree method, and local search is implemented in interpolation. Numerical examples show that the present method has high computational efficiency and good accuracy in solving elastic dynamic problems.

Fluid-structure interaction analysis by coupled FE-SPH model based on a novel searching algorithm

Fluid–Structure Interaction (FSI) problem is significant in science and engineering, which leads to challenges for computational mechanics. The coupled model of Finite Element and Smoothed Particle Hydrodynamics (FE-SPH) is a robust technique for simulation of FSI problems. However, two important steps of neighbor searching and contact searching in the coupled FE-SPH model are extremely time-consuming. Point-In-Box (PIB) searching algorithm has been developed by Swegle to improve the efficiency of searching. However, it has a shortcoming that efficiency of searching can be significantly affected by the distribution of points (nodes in FEM and particles in SPH). In this paper, in order to improve the efficiency of searching, a novel Striped-PIB (S-PIB) searching algorithm is proposed to overcome the shortcoming of PIB algorithm that caused by points distribution, and the two time-consuming steps of neighbor searching and contact searching are integrated into one searching step. The accuracy and efficiency of the newly developed searching algorithm is studied on by efficiency test and FSI problems. It has been found that the newly developed model can significantly improve the computational efficiency and it is believed to be a powerful tool for the FSI analysis.

Revolute joint approach to model joint mechanism in water-filled road safety barriers

Portable water-filled road barriers (PWFB) are roadside structures placed on temporary construction zones to separate work site from traffic. Recent changes in governing standards require PWFB to adhere to strict compliance in terms of lateral displacement and vehicle redirectionality. Actual PWFB test can be very costly, thus researchers resort to Finite Element Analysis (FEA) in the initial designs phase. There has been many research conducted on concrete barriers and flexible steel barriers using FEA, however not many was done pertaining to PWFB. This research probes a new technique to model joints in PWFB. Two methods to model the joining mechanism are presented and discussed in relation to its practicality and accuracy. Moreover, the study of the physical gap and mass of the barrier was investigated. Outcome from this research will benefit PWFB research and allow road barrier designers better knowledge in developing the next generation of road safety structures.

Direct evidence for base-mediated decomposition of alkyl hydroperoxides (ROOH) in the gas phase

Alkyl hydroperoxides (ROOH) are attributed a key role in the biochemical oxidation of lipids during oxidative stress.1 In this chemistry ROOH compounds, where the R groups are unsaturated fatty acids, are viewed as transient ntermediates which are readily degraded, due to the lability of the RO-OH bond, to yield potentially genotoxic aldehydes and ketones.2 Generally, the decomposition of alkyl hydroperoxides is thought to be mediated by radical abstraction or electron transfer processes usually involving enzymes, transition metals, or recently, Vitamin C.3 In this paper we present the first unambiguous experimental and computational evidence for base-mediated heterolytic decomposition of simple alkyl hydroperoxides by the mechanism outlined in Scheme 1.

Direct observation of the gas phase reaction of the cyclohexyl radical with dioxygen using a distonic radical ion approach

Alkylperoxyl radicals are intermediates in the oxidation Of hydrocarbons. The reactive nature of these intermediates, however, has made therin elusive to direct observation and isolation. We have employed ion trap mass spectrometry to synthesize and characterize 4-carboxylatocyclohexyl radical anions ((center dot)C(6)H(10)-CO(2)(-)) and observe their reactivity in the presence of dioxygen. The resulting reaction is facile (k = 1.8 x 10(-10) cm(3) molecule(-1) s(-1) or 30% of calculated collision rate) and results in (i) the addition Of O(2) to form stabilized 4-carboxylatocyclohexylperoxyl radical anions ((center dot)OO-C(6)H(10)-CO(2)(-)), providing the first direct observation of a cyclohexylperoxyl radical, and (ii) elimination of HO(2)(center dot) and HO(center dot) radicals consistent with recent laser-induced fluorescence studies of the reaction of neutral cyclohexyl radicals with O(2). Electronic structure calculations at the B3LYP/6-31+G(d) level of theory reveal viable pathways for the observed reactions showing that formation of the peroxyl radical is exothermic by 37 kcal mol(-1) with subsequent transition states its low as -6.6 kcal mol(-1) (formation of HO(2)(center dot)) and -9.1 kcal mol(-1) (formation of HO(center dot)) with respect to the entrance channel. The combined computational and experimental data Suggest that the structures of the reaction products correspond to cyclohexenes and epoxides from HO(2)(center dot) and HO(center dot) loss, respectively, while alternative pathways leading to cyclohexanone or ring-opened isomers ate not observed, Activation of the charged peroxyl radical (center dot)OO-C(6)H(10)-CO(2)(-) by collision induced disassociation also results in the loss Of HO(2)(center dot) and HO(center dot) radicals confirming that these products are directly connected to the peroxyl radical intermediate.

Magnetic convection heat transfer in an open ended enclosure filled with paramagnetic fluids

Numerical simulations of thermomagnetic convection of paramagnetic fluids placed in a micro-gravity condition (g nearly 0) and under a uniform vertical gradient magnetic field in an open ended square enclosure with ramp heating temperature condition applied on a vertical wall is investigated in this study. In presence of the strong magnetic gradient field thermal convection of the paramagnetic fluid might take place even in a zero-gravity environment as a direct consequence of temperature differences occurring within the fluid. The thermal boundary layer develops adjacent to the hot wall as soon as the ramp temperature condition is applied on it. There are two scenario that can be observed based on the ramp heating time. The steady state of the thermal boundary layer can be reached before the ramp time is finished or vice versa. If the ramp time is larger than the quasi-steady time then the thermal boundary layer is in a quasi-steady mode with convection balancing conduction after the quasi-steady time. Further increase of the heat input simply accelerates the flow to maintain the proper thermal balance. Finally, the boundary layer becomes completely steady state when the ramp time is finished. Effects of magnetic Rayleigh number, Prandtl number and paramagnetic fluid parameter on the flow pattern and heat transfer are presented.

The loss of carbon dioxide from activated perbenzoate anions in the gas phase : Unimolecular rearrangement via epoxidation of the benzene ring

The unimolecular reactivities of a range of perbenzoate anions (X-C6H5CO3-), including the perbenzoate anion itself (X=H), nitroperbenzoates (X=para-, meta-, ortho-NO2), and methoxyperbenzoates (X=para-, meta-OCH3) were investigated in the gas phase by electrospray ionization tandem mass spectrometry. The collision-induced dissociation mass spectra of these compounds reveal product ions consistent with a major loss of carbon dioxide requiring unimolecular rearrangement of the perbenzoate anion prior to fragmentation. Isotopic labeling of the perbenzoate anion supports rearrangement via an initial nucleophilic aromatic substitution at the ortho carbon of the benzene ring, while data from substituted perbenzoates indicate that nucleophilic attack at the ipso carbon can be induced in the presence of electron-withdrawing moieties at the ortho and para positions. Electronic structure calculations carried out at the B3LYP/6311++G(d,p) level of theory reveal two competing reaction pathways for decarboxylation of perbenzoate anions via initial nucleophilic substitution at the ortho and ipso positions, respectively. Somewhat surprisingly, however, the computational data indicate that the reaction proceeds in both instances via epoxidation of the benzene ring with decarboxylation resulting-at least initially-in the formation of oxepin or benzene oxide anions rather than the energetically favored phenoxide anion. As such, this novel rearrangement of perbenzoate anions provides an intriguing new pathway for epoxidation of the usually inert benzene ring.

Computation of ECG signal features using MCMC modelling in software and FPGA reconfigurable hardware

Computational optimisation of clinically important electrocardiogram signal features, within a single heart beat, using a Markov-chain Monte Carlo (MCMC) method is undertaken. A detailed, efficient data-driven software implementation of an MCMC algorithm has been shown. Initially software parallelisation is explored and has been shown that despite the large amount of model parameter inter-dependency that parallelisation is possible. Also, an initial reconfigurable hardware approach is explored for future applicability to real-time computation on a portable ECG device, under continuous extended use.