The simulation of stress fibre and focal adhesion development in cells on patterned substrates.

The remodelling of the cytoskeleton and focal adhesion (FA) distributions for cells on substrates with micro-patterned ligand patches is investigated using a bio-chemo-mechanical model. We investigate the effect of ligand pattern shape on the cytoskeletal arrangements and FA distributions for cells having approximately the same area. The cytoskeleton model accounts for the dynamic rearrangement of the actin/myosin stress fibres. It entails the highly nonlinear interactions between signalling, the kinetics of tension-dependent stress-fibre formation/dissolution and stress-dependent contractility. This model is coupled with another model that governs FA formation and accounts for the mechano-sensitivity of the adhesions from thermodynamic considerations. This coupled modelling scheme is shown to capture a variety of key experimental observations including: (i) the formation of high concentrations of stress fibres and FAs at the periphery of circular and triangular, convex-shaped ligand patterns; (ii) the development of high FA concentrations along the edges of the V-, T-, Y- and U-shaped concave ligand patterns; and (iii) the formation of highly aligned stress fibres along the non-adhered edges of cells on the concave ligand patterns. When appropriately calibrated, the model also accurately predicts the radii of curvature of the non-adhered edges of cells on the concave-shaped ligand patterns.

Bayesian and L1 Approaches to Sparse Unsupervised Learning

The use of L1 regularisation for sparse learning has generated immense research interest, with successful application in such diverse areas as signal acquisition, image coding, genomics and collaborative filtering. While existing work highlights the many advantages of L1 methods, in this paper we find that L1 regularisation often dramatically underperforms in terms of predictive performance when compared with other methods for inferring sparsity. We focus on unsupervised latent variable models, and develop L1 minimising factor models, Bayesian variants of "L1", and Bayesian models with a stronger L0-like sparsity induced through spike-and-slab distributions. These spike-and-slab Bayesian factor models encourage sparsity while accounting for uncertainty in a principled manner and avoiding unnecessary shrinkage of non-zero values. We demonstrate on a number of data sets that in practice spike-and-slab Bayesian methods outperform L1 minimisation, even on a computational budget. We thus highlight the need to re-assess the wide use of L1 methods in sparsity-reliant applications, particularly when we care about generalising to previously unseen data, and provide an alternative that, over many varying conditions, provides improved generalisation performance.

Numerical simulations of unsteady wet steam flows with non-equilibrium condensation in the nozzle and the steam turbine

Numerical techniques for non-equilibrium condensing flows are presented. Conservation equations for homogeneous gas-liquid two-phase compressible flows are solved by using a finite volume method based on an approximate Riemann solver. The phase change consists of the homogeneous nucleation and growth of existing droplets. Nucleation is computed with the classical Volmer-Frenkel model, corrected for the influence of the droplet temperature being higher than the steam temperature due to latent heat release. For droplet growth, two types of heat transfer model between droplets and the surrounding steam are used: a free molecular flow model and a semi-empirical two-layer model which is deemed to be valid over a wide range of Knudsen number. The computed pressure distribution and Sauter mean droplet diameters in a convergent-divergent (Laval) nozzle are compared with experimental data. Both droplet growth models capture qualitatively the pressure increases due to sudden heat release by the non-equilibrium condensation. However the agreement between computed and experimental pressure distributions is better for the two-layer model. The droplet diameter calculated by this model also agrees well with the experimental value, whereas that predicted by the free molecular model is too small. Condensing flows in a steam turbine cascade are calculated at different Mach numbers and inlet superheat conditions and are compared with experiments. Static pressure traverses downstream from the blade and pressure distributions on the blade surface agree well with experimental results in all cases. Once again, droplet diameters computed with the two-layer model give best agreement with the experiments. Droplet sizes are found to vary across the blade pitch due to the significant variation in expansion rate. Flow patterns including oblique shock waves and condensation-induced pressure increases are also presented and are similar to those shown in the experimental Schlieren photographs. Finally, calculations are presented for periodically unsteady condensing flows in a low expansion rate, convergent-divergent (Laval) nozzle. Depending on the inlet stagnation subcooling, two types of self-excited oscillations appear: a symmetric mode at lower inlet subcooling and an asymmetric mode at higher subcooling. Plots of oscillation frequency versus inlet sub-cooling exhibit a hysteresis loop, in accord with observations made by other researchers for moist air flow. Copyright © 2006 by ASME.

Scalar and its dissipation in the near field of turbulent lifted jet flame

In this study various scalar dissipation rates and their modelling in the context of partially premixed flame are investigated. A DNS dataset of the near field of a turbulent hydrogen lifted jet flame is processed to analyse the mixture fraction and progress variable dissipation rates and their cross dissipation rate at several axial positions. It is found that the classical model for the passive scalar dissipation rate ε{lunate}̃ZZ gives good agreement with the DNS, while models developed based on premixed flames for the reactive scalar dissipation rate ε{lunate}̃cc only qualitatively capture the correct trend. The cross dissipation rate ε{lunate}̃cZ is mostly negative and can be reasonably approximated at downstream positions once ε{lunate}̃ZZ and ε{lunate}̃cc are known, although the sign cannot be determined. This approach gives better results than one employing a constant ratio of turbulent timescale and the scalar covariance c'Z'̃. The statistics of scalar gradients are further examined and lognormal distributions are shown to be very good approximations for the passive scalar and acceptable for the reactive scalar. The correlation between the two gradients increases downstream as the partially premixed flame in the near field evolves ultimately to a diffusion flame in the far field. A bivariate lognormal distribution is tested and found to be a reasonable approximation for the joint PDF of the two scalar gradients. © 2011 The Combustion Institute.

Internal representations of temporal statistics and feedback calibrate motor-sensory interval timing.

Humans have been shown to adapt to the temporal statistics of timing tasks so as to optimize the accuracy of their responses, in agreement with the predictions of Bayesian integration. This suggests that they build an internal representation of both the experimentally imposed distribution of time intervals (the prior) and of the error (the loss function). The responses of a Bayesian ideal observer depend crucially on these internal representations, which have only been previously studied for simple distributions. To study the nature of these representations we asked subjects to reproduce time intervals drawn from underlying temporal distributions of varying complexity, from uniform to highly skewed or bimodal while also varying the error mapping that determined the performance feedback. Interval reproduction times were affected by both the distribution and feedback, in good agreement with a performance-optimizing Bayesian observer and actor model. Bayesian model comparison highlighted that subjects were integrating the provided feedback and represented the experimental distribution with a smoothed approximation. A nonparametric reconstruction of the subjective priors from the data shows that they are generally in agreement with the true distributions up to third-order moments, but with systematically heavier tails. In particular, higher-order statistical features (kurtosis, multimodality) seem much harder to acquire. Our findings suggest that humans have only minor constraints on learning lower-order statistical properties of unimodal (including peaked and skewed) distributions of time intervals under the guidance of corrective feedback, and that their behavior is well explained by Bayesian decision theory.

A derivation of the source-channel error exponent using nonidentical product distributions

This paper studies the random-coding exponent of joint source-channel coding for a scheme where source messages are assigned to disjoint subsets (referred to as classes), and codewords are independently generated according to a distribution that depends on the class index of the source message. For discrete memoryless systems, two optimally chosen classes and product distributions are found to be sufficient to attain the sphere-packing exponent in those cases where it is tight. © 2014 IEEE.

Discrete dislocation plasticity analysis of crack-tip fields in polycrystalline materials

Small scale yielding around a mode I crack is analysed using polycrystalline discrete dislocation plasticity. Plane strain analyses are carried out with the dislocations all of edge character and modelled as line singularities in a linear elastic material. The lattice resistance to dislocation motion, nucleation, interaction with obstacles and annihilation are incorporated through a set of constitutive rules. Grain boundaries are modelled as impenetrable to dislocations. The polycrystalline material is taken to consist of two types of square grains, one of which has a bcc-like orientation and the other an fcc-like orientation. For both orientations there are three active slip systems. Alternating rows, alternating columns and a checker-board-like arrangement of the grains is used to construct the polycrystalline materials. Consistent with the increasing yield strength of the polycrystalline material with decreasing grain size, the calculations predict a decrease in both the plastic zone size and the crack-tip opening displacement for a given applied mode I stress intensity factor. Furthermore, slip-band and kink-band formation is inhibited by all grain arrangements and, with decreasing grain size, the stress and strain distributions more closely resemble the HRR fields with the crack-tip opening approximately inversely proportional to the yield strength of the polycrystalline materials. The calculations predict a reduction in fracture toughness with decreasing grain size associated with the grain boundaries acting as effective barriers to dislocation motion.

QM/MM simulation of liquid water with an adaptive quantum region.

The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.

Tsunami wave runup on the clustered islands using boussinesq-type model

This paper describes the implementation of the Boussinesq-type model and extends its application to the tsunami wave runup on the clustered islands (multiple adjacent conical islands), in turn, an extensively validated two-dimensional Boussinesq-type model is employed to examine the interaction between a propagating solitary wave and multiple idealised conical islands, with particular emphasis on a combination effect of two adjustable parameters for spacing interval/diameter ratio between the adjacent conical islands, S/D, and the rotating angle of the structural configuration,θ on maximum soliton runup heights. An extensive parameter study concerning the combination effect of alteringθ and S/D on the maximum soliton runup with the multi-conical islands is subsequently carried out and the distributions of the maximum runup heights on each conical island are obtained and compared for the twin-island cases. The worst case study is performed for each case in respect of the enhancement in the maximum wave runup heights by the multi-conical islands. It is found that the nonlinear wave diffraction, reflection and refraction play a significant role in varying the maximum soliton runup heights on multiconical islands. The comparatively large maximum soliton runups are generally predicted for the merged and bottom mounted clusteredislands. Furthermore, the joints of the clustered-merged islands are demonstrated to suffer the most of the tsunami wave attack. The conical islands that position in the shadow regions behind the surrounding islands are found to withstand relatively less extreme wave impact. Although, these numerical investigations are considerable simplifications of the multi conical islands, they give a critical insight into certain important hydrodynamic characteristics of the interaction between an extreme wave event and a group of clustered conical islands, and thus providing a useful engineering guidance for extreme wave mitigation and coastal development. Copyright © 2012 by the International Society of Offshore and Polar Engineers (ISOPE).

Factor analysis based VTS discriminative adaptive training

Vector Taylor Series (VTS) model based compensation is a powerful approach for noise robust speech recognition. An important extension to this approach is VTS adaptive training (VAT), which allows canonical models to be estimated on diverse noise-degraded training data. These canonical model can be estimated using EM-based approaches, allowing simple extensions to discriminative VAT (DVAT). However to ensure a diagonal corrupted speech covariance matrix the Jacobian (loading matrix) relating the noise and clean speech is diagonalised. In this work an approach for yielding optimal diagonal loading matrices based on minimising the expected KL-divergence between the diagonal loading matrix and "correct" distributions is proposed. The performance of DVAT using the standard and optimal diagonalisation was evaluated on both in-car collected data and the Aurora4 task. © 2012 IEEE.