Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

A principled approach to interactive hierarchical non-linear visualization of high-dimensional data

Hierarchical visualization systems are desirable because a single two-dimensional visualization plot may not be sufficient to capture all of the interesting aspects of complex high-dimensional data sets. We extend an existing locally linear hierarchical visualization system PhiVis [1] in several directions: bf(1) we allow for em non-linear projection manifolds (the basic building block is the Generative Topographic Mapping -- GTM), bf(2) we introduce a general formulation of hierarchical probabilistic models consisting of local probabilistic models organized in a hierarchical tree, bf(3) we describe folding patterns of low-dimensional projection manifold in high-dimensional data space by computing and visualizing the manifold's local directional curvatures. Quantities such as magnification factors [3] and directional curvatures are helpful for understanding the layout of the nonlinear projection manifold in the data space and for further refinement of the hierarchical visualization plot. Like PhiVis, our system is statistically principled and is built interactively in a top-down fashion using the EM algorithm. We demonstrate the visualization system principle of the approach on a complex 12-dimensional data set and mention possible applications in the pharmaceutical industry.

Computational mechanics of molecular systems:quantifying high-dimensional dynamics by distribution of Poincaré recurrence times

A framework that connects computational mechanics and molecular dynamics has been developed and described. As the key parts of the framework, the problem of symbolising molecular trajectory and the associated interrelation between microscopic phase space variables and macroscopic observables of the molecular system are considered. Following Shalizi and Moore, it is shown that causal states, the constituent parts of the main construct of computational mechanics, the e-machine, define areas of the phase space that are optimal in the sense of transferring information from the micro-variables to the macro-observables. We have demonstrated that, based on the decay of their Poincare´ return times, these areas can be divided into two classes that characterise the separation of the phase space into resonant and chaotic areas. The first class is characterised by predominantly short time returns, typical to quasi-periodic or periodic trajectories. This class includes a countable number of areas corresponding to resonances. The second class includes trajectories with chaotic behaviour characterised by the exponential decay of return times in accordance with the Poincare´ theorem.

Estimation of uncertainty in three-dimensional coordinate measurement by comparison with calibrated points

This paper details a method of estimating the uncertainty of dimensional measurement for a three-dimensional coordinate measurement machine. An experimental procedure was developed to compare three-dimensional coordinate measurements with calibrated reference points. The reference standard used to calibrate these reference points was a fringe counting interferometer with a multilateration-like technique employed to establish three-dimensional coordinates. This is an extension of the established technique of comparing measured lengths with calibrated lengths. Specifically a distributed coordinate measurement device was tested which consisted of a network of Rotary-Laser Automatic Theodolites (R-LATs), this system is known commercially as indoor GPS (iGPS). The method was found to be practical and was used to estimate that the uncertainty of measurement for the basic iGPS system is approximately 1 mm at a 95% confidence level throughout a measurement volume of approximately 10 m × 10 m × 1.5 m. © 2010 IOP Publishing Ltd.

A hierarchical latent variable model for data visualization

Visualization has proven to be a powerful and widely-applicable tool the analysis and interpretation of data. Most visualization algorithms aim to find a projection from the data space down to a two-dimensional visualization space. However, for complex data sets living in a high-dimensional space it is unlikely that a single two-dimensional projection can reveal all of the interesting structure. We therefore introduce a hierarchical visualization algorithm which allows the complete data set to be visualized at the top level, with clusters and sub-clusters of data points visualized at deeper levels. The algorithm is based on a hierarchical mixture of latent variable models, whose parameters are estimated using the expectation-maximization algorithm. We demonstrate the principle of the approach first on a toy data set, and then apply the algorithm to the visualization of a synthetic data set in 12 dimensions obtained from a simulation of multi-phase flows in oil pipelines and to data in 36 dimensions derived from satellite images.

GTM: the generative topographic mapping

This thesis describes the Generative Topographic Mapping (GTM) --- a non-linear latent variable model, intended for modelling continuous, intrinsically low-dimensional probability distributions, embedded in high-dimensional spaces. It can be seen as a non-linear form of principal component analysis or factor analysis. It also provides a principled alternative to the self-organizing map --- a widely established neural network model for unsupervised learning --- resolving many of its associated theoretical problems. An important, potential application of the GTM is visualization of high-dimensional data. Since the GTM is non-linear, the relationship between data and its visual representation may be far from trivial, but a better understanding of this relationship can be gained by computing the so-called magnification factor. In essence, the magnification factor relates the distances between data points, as they appear when visualized, to the actual distances between those data points. There are two principal limitations of the basic GTM model. The computational effort required will grow exponentially with the intrinsic dimensionality of the density model. However, if the intended application is visualization, this will typically not be a problem. The other limitation is the inherent structure of the GTM, which makes it most suitable for modelling moderately curved probability distributions of approximately rectangular shape. When the target distribution is very different to that, theaim of maintaining an `interpretable' structure, suitable for visualizing data, may come in conflict with the aim of providing a good density model. The fact that the GTM is a probabilistic model means that results from probability theory and statistics can be used to address problems such as model complexity. Furthermore, this framework provides solid ground for extending the GTM to wider contexts than that of this thesis.

Gas distribution in shallow packed beds

Packed beds have many industrial applications and are increasingly used in the process industries due to their low pressure drop. With the introduction of more efficient packings, novel packing materials (i.e. adsorbents) and new applications (i.e. flue gas desulphurisation); the aspect ratio (height to diameter) of such beds is decreasing. Obtaining uniform gas distribution in such beds is of crucial importance in minimising operating costs and optimising plant performance. Since to some extent a packed bed acts as its own distributor the importance of obtaining uniform gas distribution has increased as aspect ratios (bed height to diameter) decrease. There is no rigorous design method for distributors due to a limited understanding of the fluid flow phenomena and in particular of the effect of the bed base / free fluid interface. This study is based on a combined theoretical and modelling approach. The starting point is the Ergun Equation which is used to determine the pressure drop over a bed where the flow is uni-directional. This equation has been applied in a vectorial form so it can be applied to maldistributed and multi-directional flows and has been realised in the Computational Fluid Dynamics code PHOENICS. The use of this equation and its application has been verified by modelling experimental measurements of maldistributed gas flows, where there is no free fluid / bed base interface. A novel, two-dimensional experiment has been designed to investigate the fluid mechanics of maldistributed gas flows in shallow packed beds. The flow through the outlet of the duct below the bed can be controlled, permitting a rigorous investigation. The results from this apparatus provide useful insights into the fluid mechanics of flow in and around a shallow packed bed and show the critical effect of the bed base. The PHOENICS/vectorial Ergun Equation model has been adapted to model this situation. The model has been improved by the inclusion of spatial voidage variations in the bed and the prescription of a novel bed base boundary condition. This boundary condition is based on the logarithmic law for velocities near walls without restricting the velocity at the bed base to zero and is applied within a turbulence model. The flow in a curved bed section, which is three-dimensional in nature, is examined experimentally. The effect of the walls and the changes in gas direction on the gas flow are shown to be particularly significant. As before, the relative amounts of gas flowing through the bed and duct outlet can be controlled. The model and improved understanding of the underlying physical phenomena form the basis for the development of new distributors and rigorous design methods for them.

Using organoclay to promote morphology refinement and co-continuity in high-density polyethylene/polyamide 6 blends - Effect of filler content and polymer matrix composition

We investigate the gradual changes of the microstructure of two blends of high-density polyethylene (HDPE) and polyamide 6 (PA6) at opposite composition filled with increasing amounts of an organomodified clay. The filler locates preferentially inside the polyamide phase, bringing about radical alterations in the micron-scale arrangement of the polymer phases. When the host polyamide represents the major constituent, a sudden reduction of the average sizes of the polyethylene droplets was observed upon addition of even low amounts of organoclay. A morphology refinement was also noticed at low filler contents when the particles distributes inside the minor phase. In this case, however, keep increasing the organoclay content eventually results in a high degree of PA6 phase continuity. Rheological analyses reveal that the filler loading at which the polyamide assembles in a continuous network corresponds to the critical threshold for its rheological transition from a liquid- to a gel-like behaviour, which is indicative of the structuring of the filler inside the host PA6. On the basis of this finding, a schematic mechanism is proposed in which the role of the filler in driving the space arrangement of the polymer phases is discussed. Finally, we show that the synergism between the reinforcing action of the filler and its ability to affect the blend microstructure can be exploited in order to enhance relevant technological properties of the materials, such as their high temperature structural integrity.

Spatiotemporal optical bullets in two-dimensional fiber arrays and their stability

Long-lived light bullets fully localized in both space and time can be generated in novel photonic media such as multicore optical fiber or waveguide arrays. In this paper we present detailed theoretical analysis on the existence and stability of the discrete-continuous light bullets using a very generic model that occurs in a number of applications.

The effects of material variations in high value manufacturing industries

It has never been easy for manufacturing companies to understand their confidence level in terms of how accurate and to what degree of flexibility parts can be made. This brings uncertainty in finding the most suitable manufacturing method as well as in controlling their product and process verification systems. The aim of this research is to develop a system for capturing the company’s knowledge and expertise and then reflect it into an MRP (Manufacturing Resource Planning) system. A key activity here is measuring manufacturing and machining capabilities to a reasonable confidence level. For this purpose an in-line control measurement system is introduced to the company. Using SPC (Statistical Process Control) not only helps to predict the trend in manufacturing of parts but also minimises the human error in measurement. Gauge R&R (Repeatability and Reproducibility) study identifies problems in measurement systems. Measurement is like any other process in terms of variability. Reducing this variation via an automated machine probing system helps to avoid defects in future products.Developments in aerospace, nuclear, oil and gas industries demand materials with high performance and high temperature resistance under corrosive and oxidising environments. Superalloys were developed in the latter half of the 20th century as high strength materials for such purposes. For the same characteristics superalloys are considered as difficult-to-cut alloys when it comes to formation and machining. Furthermore due to the sensitivity of superalloy applications, in many cases they should be manufactured with tight tolerances. In addition superalloys, specifically Nickel based, have unique features such as low thermal conductivity due to having a high amount of Nickel in their material composition. This causes a high surface temperature on the work-piece at the machining stage which leads to deformation in the final product.Like every process, the material variations have a significant impact on machining quality. The main cause of variations can originate from chemical composition and mechanical hardness. The non-uniform distribution of metal elements is a major source of variation in metallurgical structures. Different heat treatment standards are designed for processing the material to the desired hardness levels based on application. In order to take corrective actions, a study on the material aspects of superalloys has been conducted. In this study samples from different batches of material have been analysed. This involved material preparation for microscopy analysis, and the effect of chemical compositions on hardness (before and after heat treatment). Some of the results are discussed and presented in this paper.

Jointly event extraction and visualization on Twitter via probabilistic modelling

Event extraction from texts aims to detect structured information such as what has happened, to whom, where and when. Event extraction and visualization are typically considered as two different tasks. In this paper, we propose a novel approach based on probabilistic modelling to jointly extract and visualize events from tweets where both tasks benefit from each other. We model each event as a joint distribution over named entities, a date, a location and event-related keywords. Moreover, both tweets and event instances are associated with coordinates in the visualization space. The manifold assumption that the intrinsic geometry of tweets is a low-rank, non-linear manifold within the high-dimensional space is incorporated into the learning framework using a regularization. Experimental results show that the proposed approach can effectively deal with both event extraction and visualization and performs remarkably better than both the state-of-the-art event extraction method and a pipeline approach for event extraction and visualization.