Numerical investigation of the active role of the actin cytoskeleton in the compression resistance of cells.

Numerous in-vitro studies have established that cells react to their physical environment and to applied mechanical loading. However, the mechanisms underlying such phenomena are poorly understood. Previous modelling of cell compression considered the cell as a passive homogenous material, requiring an artificial increase in the stiffness of spread cells to replicate experimentally measured forces. In this study, we implement a fully 3D active constitutive formulation that predicts the distribution, remodelling, and contractile behaviour of the cytoskeleton. Simulations reveal that polarised and axisymmetric spread cells contain stress fibres which form dominant bundles that are stretched during compression. These dominant fibres exert tension; causing an increase in computed compression forces compared to round cells. In contrast, fewer stress fibres are computed for round cells and a lower resistance to compression is predicted. The effect of different levels of cellular contractility associated with different cell phenotypes is also investigated. Highly contractile cells form more dominant circumferential stress fibres and hence provide greater resistance to compression. Computed predictions correlate strongly with published experimentally observed trends of compression resistance as a function of cellular contractility and offer an insight into the link between cell geometry, stress fibre distribution and contractility, and cell deformability. Importantly, it is possible to capture the behaviour of both round and spread cells using a given, unchanged set of material parameters for each cell type. Finally, it is demonstrated that stress distributions in the cell cytoplasm and nucleus computed using the active formulation differ significantly from those computed using passive material models.

Experimental and numerical investigation of fracture mechanics of bitumen beams

This work presents an experimental and numerical investigation to characterise the fracture properties of pure bitumen (the binder in asphalt paving materials). The paper is divided into two parts. The first part describes an experimental study of fracture characterisation parameters of pure bitumen as determined by three-point bend tests. The second part deals with modelling of fracture and failure of bitumen by Finite Element analysis. Fracture mechanics parameters, stress intensity factor, KIC, fracture energy, GIC, and J-integral, JIC, are used for evaluation of bitumen's fracture properties. The material constitutive model developed by Ossa et al. [40,41] which was implemented into a FE code by Costanzi [18] is combined with cohesive zone models (CZM) to simulate the fracture behaviour of pure bitumen. Experimental and numerical results are presented in the form of failure mechanism maps where ductile, brittle and brittle-ductile transition regimes of fracture behaviour are classified. The FE predictions of fracture behaviour match well with experimental results. © 2012 Elsevier Ltd.

Cellular contractility and substrate elasticity: A numerical investigation of the actin cytoskeleton and cell adhesion

Numerous experimental studies have established that cells can sense the stiffness of underlying substrates and have quantified the effect of substrate stiffness on stress fibre formation, focal adhesion area, cell traction, and cell shape. In order to capture such behaviour, the current study couples a mixed mode thermodynamic and mechanical framework that predicts focal adhesion formation and growth with a material model that predicts stress fibre formation, contractility, and dissociation in a fully 3D implementation. Simulations reveal that SF contractility plays a critical role in the substrate-dependent response of cells. Compliant substrates do not provide sufficient tension for stress fibre persistence, causing dissociation of stress fibres and lower focal adhesion formation. In contrast, cells on stiffer substrates are predicted to contain large amounts of dominant stress fibres. Different levels of cellular contractility representative of different cell phenotypes are found to alter the range of substrate stiffness that cause the most significant changes in stress fibre and focal adhesion formation. Furthermore, stress fibre and focal adhesion formation evolve as a cell spreads on a substrate and leading to the formation of bands of fibres leading from the cell periphery over the nucleus. Inhibiting the formation of FAs during cell spreading is found to limit stress fibre formation. The predictions of this mutually dependent material-interface framework are strongly supported by experimental observations of cells adhered to elastic substrates and offer insight into the inter-dependent biomechanical processes regulating stress fibre and focal adhesion formation. © 2013 Springer-Verlag Berlin Heidelberg.

Experimental and numerical investigation of the seismic behavior of rectangular tunnels in soft soils

Underground structures constitute crucial components of the transportation networks. Considering their significance for modern societies, their proper seismic design is of great importance. However, this design may become very tricky, accounting of the lack of knowledge regarding their seismic behavior. Several issues that are significantly affecting this behavior (i.e. earth pressures on the structure, seismic shear stresses around the structure, complex deformation modes for rectangular structures during shaking etc.) are still open. The problem is wider for the non-circular (i.e. rectangular) structures, were the soilstructure interaction effects are expected to be maximized. The paper presents representative experimental results from a test case of a series of dynamic centrifuge tests that were performed on rectangular tunnels embedded in dry sand. The tests were carried out at the centrifuge facility of the University of Cambridge, within the Transnational Task of the SERIES EU research program. The presented test case is also numerically simulated and studied. Preliminary full dynamic time history analyses of the coupled soil-tunnel system are performed, using ABAQUS. Soil non-linearity and soil-structure interaction are modeled, following relevant specifications for underground structures and tunnels. Numerical predictions are compared to experimental results and discussed. Based on this comprehensive experimental and numerical study, the seismic behavior of rectangular embedded structures is better understood and modeled, consisting an important step in the development of appropriate specifications for the seismic design of rectangular shallow tunnels.

Numerical investigation of particle velocity distributions in aeolian sand transport

Particle velocity distribution in a blowing sand cloud is a reflection of saltation movement of many particles. Numerical analysis is performed for particle velocity distribution with a discrete particle model. The probability distributions of resultant particle velocity in the impact-entrainment process, particle horizontal and vertical velocities at different heights and the vertical velocity of ascending particles are analyzed. The probability distributions of resultant impact and lift-off velocities of saltating particles can be expressed by a log-normal function, and that of impact angle comply with an exponential function. The probability distribution of particle horizontal and vertical velocities at different heights shows a typical single-peak pattern. In the lower part of saltation layer, the particle horizontal velocity distribution is positively skewed. Further analysis shows that the probability density function of the vertical velocity of ascending particles is similar to the right-hand part of a normal distribution function, and a general equation is acquired for the probability density function of non-dimensional vertical velocity of ascending particles which is independent of diameter of saltating particles, wind strength and height. These distributions in the present numerical analysis are consistent with reported experimental results. The present investigation is important for understanding the saltation state in wind-blown sand movement. (C) 2009 Elsevier B.V. All rights reserved.

Numerical investigation of nutrient limitations in the Bohai Sea

River discharges are the important freshwater and nutrient sources for Bohai Sea (BS), and have a profound impact on the local marine environment. In this paper, the annual cycles of nutrient and phytoplankton dynamics in 1980s were reproduced using a coupled biogeochemical-physical model. Based on the validated simulations, the nutrient limitation characters were further investigated by running the model with the riverine nutrient altered, first enriching nitrogen and then phosphorus. It was found that although the riverine N:P ratios in Yellow and Haihe Rivers were much higher than the Redfield number, the nitrogen enrichment was still able to enhance the algae bloom in Laizhou and Bohai Bays. On the other hand, the response of algae growth to phosphorus enrichment was not thus obvious, which suggests that the local phytoplankton dynamics was characterized by the nitrogen limitation. Simulations also show that the nitrogen enrichment is generally accompanied by the phosphorus consumption, so a shift from nitrogen limitation to phosphorus limitation may occur if such a trend continues. (C) 2010 Elsevier Ltd. All rights reserved.

A two-dimensional numerical investigation of the oscillatory flow behaviour in rectangular fire compartments with a single horizontal ceiling vent

This paper presents a comparison of fire field model predictions with experiment for the case of a fire within a compartment which is vented (buoyancydriven) to the outside by a single horizontal ceiling vent. Unlike previous work, the mathematical model does not employ a mixing ratio to represent vent temperatures but allows the model to predict vent temperatures a priori. The experiment suggests that the flow through the vent produces oscillatory behaviour in vent temperatures with puffs of smoke emerging from the fire compartment. This type of flow is also predicted by the fire field model. While the numerical predictions are in good qualitative agreement with observations, they overpredict the amplitudes of the temperature oscillations within the vent and also the compartment temperatures. The discrepancies are thought to be due to three-dimensional effects not accounted for in this model as well as using standard ‘practices’ normally used by the community with regards to discretization and turbulence models. Furthermore, it is important to note that the use of the k–ε turbulence model in a transient mode, as is used here, may have a significant effect on the results. The numerical results also suggest that a linear relationship exists between the frequency of vent temperature oscillation (n) and the heat release rate (Q0) of the type n∝Q0.290, similar to that observed for compartments with two horizontal vents. This relationship is predicted to occur only for heat release rates below a critical value. Furthermore, the vent discharge coefficient is found to vary in an oscillatory fashion with a mean value of 0.58. Below the critical heat release rate the mean discharge coefficient is found to be insensitive to fire size.

Numerical investigation of a source extraction technique based on an acoustic correction method

An aerodynamic sound source extraction from a general flow field is applied to a number of model problems and to a problem of engineering interest. The extraction technique is based on a variable decomposition, which results to an acoustic correction method, of each of the flow variables into a dominant flow component and a perturbation component. The dominant flow component is obtained with a general-purpose Computational Fluid Dynamics (CFD) code which uses a cell-centred finite volume method to solve the Reynolds-averaged Navier–Stokes equations. The perturbations are calculated from a set of acoustic perturbation equations with source terms extracted from unsteady CFD solutions at each time step via the use of a staggered dispersion-relation-preserving (DRP) finite-difference scheme. Numerical experiments include (1) propagation of a 1-D acoustic pulse without mean flow, (2) propagation of a 2-D acoustic pulse with/without mean flow, (3) reflection of an acoustic pulse from a flat plate with mean flow, and (4) flow-induced noise generated by the an unsteady laminar flow past a 2-D cavity. The computational results demonstrate the accuracy for model problems and illustrate the feasibility for more complex aeroacoustic problems of the source extraction technique.