Simulation of glassy state relaxations in polymers: A static analysis of methyl group and methoxy group rotation in poly(vinyl methyl ether)

We show that the simple quasi-static technique, also called the adiabatic mapping technique, can be used to determine the energetics of rotation of methyl and methoxy groups in amorphous poly(vinyl methyl ether) even though the latter process is too slow to be amenable to direct molecular dynamics simulation. For the methyl group rotation, we find that the mean and standard deviation of the simulated rotational barrier heights agree well with experimental data from quasi-elastic neutron scattering. In the case of the methoxy groups we find that just 4% of the groups contribute more than 90% of the observed dielectric relaxation strength. The groups which make the most contribution are those which, by virtue of their particular conformation and local environment, have two alternative positions of similar energy.

The role of texture amplitude in shape from shading

When a textured surface is modulated in depth and illuminated, parts of the surface receive different levels of illumination; the resulting variations in luminance can be used to infer the shape of the depth modulations-shape from shading. The changes in illumination also produce changes in the amplitude of the texture, although local contrast remains constant. We investigated the role of texture amplitude in supporting shape from shading. If a luminance plaid is added to a binary noise texture (LM), shape from shading produces perception of corrugations in two directions. If the amplitude of the noise is also modulated (AM) such that it is in-phase with one of the luminance sinusoids and out-of-phase with the other, the resulting surface is seen as corrugated in only one directionöthat supported by the in-phase pairing. We confirmed this subjective report experimentally, using a depth-mapping technique. Further, we asked naïve observers to indicate the direction of corrugations in plaids made up of various combinations of LM and AM. LM+AM was seen as having most depth, then LM-only, then LM-AM, and then AM-only. Our results suggest that while LM is required to see depth from shading, its phase relative to any AM component is also important.

A study of cluster analysis techniques and their applications

This thesis seeks to describe the development of an inexpensive and efficient clustering technique for multivariate data analysis. The technique starts from a multivariate data matrix and ends with graphical representation of the data and pattern recognition discriminant function. The technique also results in distances frequency distribution that might be useful in detecting clustering in the data or for the estimation of parameters useful in the discrimination between the different populations in the data. The technique can also be used in feature selection. The technique is essentially for the discovery of data structure by revealing the component parts of the data. lhe thesis offers three distinct contributions for cluster analysis and pattern recognition techniques. The first contribution is the introduction of transformation function in the technique of nonlinear mapping. The second contribution is the us~ of distances frequency distribution instead of distances time-sequence in nonlinear mapping, The third contribution is the formulation of a new generalised and normalised error function together with its optimal step size formula for gradient method minimisation. The thesis consists of five chapters. The first chapter is the introduction. The second chapter describes multidimensional scaling as an origin of nonlinear mapping technique. The third chapter describes the first developing step in the technique of nonlinear mapping that is the introduction of "transformation function". The fourth chapter describes the second developing step of the nonlinear mapping technique. This is the use of distances frequency distribution instead of distances time-sequence. The chapter also includes the new generalised and normalised error function formulation. Finally, the fifth chapter, the conclusion, evaluates all developments and proposes a new program. for cluster analysis and pattern recognition by integrating all the new features.

Bridging large and small scales of water models using hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework

This thesis presents a two-dimensional water model investigation and development of a multiscale method for the modelling of large systems, such as virus in water or peptide immersed in the solvent. We have implemented a two-dimensional ‘Mercedes Benz’ (MB) or BN2D water model using Molecular Dynamics. We have studied its dynamical and structural properties dependence on the model’s parameters. For the first time we derived formulas to calculate thermodynamic properties of the MB model in the microcanonical (NVE) ensemble. We also derived equations of motion in the isothermal–isobaric (NPT) ensemble. We have analysed the rotational degree of freedom of the model in both ensembles. We have developed and implemented a self-consistent multiscale method, which is able to communicate micro- and macro- scales. This multiscale method assumes, that matter consists of the two phases. One phase is related to micro- and the other to macroscale. We simulate the macro scale using Landau Lifshitz-Fluctuating Hydrodynamics, while we describe the microscale using Molecular Dynamics. We have demonstrated that the communication between the disparate scales is possible without introduction of fictitious interface or approximations which reduce the accuracy of the information exchange between the scales. We have investigated control parameters, which were introduced to control the contribution of each phases to the matter behaviour. We have shown, that microscales inherit dynamical properties of the macroscales and vice versa, depending on the concentration of each phase. We have shown, that Radial Distribution Function is not altered and velocity autocorrelation functions are gradually transformed, from Molecular Dynamics to Fluctuating Hydrodynamics description, when phase balance is changed. In this work we test our multiscale method for the liquid argon, BN2D and SPC/E water models. For the SPC/E water model we investigate microscale fluctuations which are computed using advanced mapping technique of the small scales to the large scales, which was developed by Voulgarakisand et. al.

Biomaterial interactions with compromised tissue surfaces

This thesis is concerned with the nature of biomaterial interactions with compromised host tissue sites. Both ocular and dermal tissues can be wounded, following injury, disease or surgery, and consequently require the use of a biomaterial. Clear analogies exist between the cornea/tear film/contact lens and the dermal wound bed/wound fluid/skin adhesive wound dressing. The work described in this thesis builds upon established biochemistry to examine specific aspects of the interaction of biomaterials with compromised ocular and dermal tissue sites, with a particular focus on the role of vitronectin. Vitronectin is a prominent cell adhesion glycoprotein present in both tear fluid and wound fluid, and has a role in the regulation and upregulation of plasmin. The interaction of contact lenses with the cornea was assessed by a novel on-lens cell-based vitronectin assay technique. Vitronectin mapping showed that vitronectin-mediated cell adhesion to contact lens surfaces was due to the contact lens-corneal mechanical interaction rather than deposition out of the tear film. This deposition is associated predominantly with the peripheral region of the posterior contact lens surface. The locus of vitronectin deposition on the contact lens surface, which is affected by material modulus, is potentially an important factor in the generation of plasmin in the posterior tear film. Use of the vitronectin mapping technique on ex vivo bandage contact lenses revealed greater vitronectin-mediated cell adhesion to the contact lens surfaces in comparison to lenses worn in the healthy eye. The results suggest that vitronectin is more readily deposited from the impaired corneal tissue bed than the intact healthy tissue bed. Significantly, subjects with a deficient tear film were found to deposit high vitronectin-mediated cell adhesion levels to the BCL surface, thus highlighting the influence of the contact lens-tissue interaction upon deposition. Biomimetic principles imply that adhesive materials for wound applications, including hydrogels and hydrocolloids, should closely match the surface energy parameters of skin. The surface properties of hydrocolloid adhesives were found to be easily modified by contact with siliconised plastic release liners. In contrast, paper release liners did not significantly affect the adhesive surface properties. In order to characterise such materials in the actual wound environment, which is an extremely challenging task, preliminary considerations for the design of an artificial wound fluid model from an animal serum base were addressed.

A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as “histogram binning” inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. ^ Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. ^ The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. ^ These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. ^ In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation. ^

A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as "histogram binning" inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation.

Real-Time Visual SLAM Using Pre - Existing Floor Lines as Landmarks and a Single Camera

SANTANA, André M.; SANTIAGO, Gutemberg S.; MEDEIROS, Adelardo A. D. Real-Time Visual SLAM Using Pre-Existing Floor Lines as Landmarks and a Single Camera. In: CONGRESSO BRASILEIRO DE AUTOMÁTICA, 2008, Juiz de Fora, MG. Anais... Juiz de Fora: CBA, 2008.

Real-Time Visual SLAM Using Pre - Existing Floor Lines as Landmarks and a Single Camera

SANTANA, André M.; SANTIAGO, Gutemberg S.; MEDEIROS, Adelardo A. D. Real-Time Visual SLAM Using Pre-Existing Floor Lines as Landmarks and a Single Camera. In: CONGRESSO BRASILEIRO DE AUTOMÁTICA, 2008, Juiz de Fora, MG. Anais... Juiz de Fora: CBA, 2008.

An hr-adaptive discontinuous Galerkin method for advection-diffusion problems

We propose an adaptive mesh refinement strategy based on exploiting a combination of a pre-processing mesh re-distribution algorithm employing a harmonic mapping technique, and standard (isotropic) mesh subdivision for discontinuous Galerkin approximations of advection-diffusion problems. Numerical experiments indicate that the resulting adaptive strategy can efficiently reduce the computed discretization error by clustering the nodes in the computational mesh where the analytical solution undergoes rapid variation.

Least square projection: A fast high-precision multidimensional projection technique and its application to document mapping

The problem of projecting multidimensional data into lower dimensions has been pursued by many researchers due to its potential application to data analyses of various kinds. This paper presents a novel multidimensional projection technique based on least square approximations. The approximations compute the coordinates of a set of projected points based on the coordinates of a reduced number of control points with defined geometry. We name the technique Least Square Projections ( LSP). From an initial projection of the control points, LSP defines the positioning of their neighboring points through a numerical solution that aims at preserving a similarity relationship between the points given by a metric in mD. In order to perform the projection, a small number of distance calculations are necessary, and no repositioning of the points is required to obtain a final solution with satisfactory precision. The results show the capability of the technique to form groups of points by degree of similarity in 2D. We illustrate that capability through its application to mapping collections of textual documents from varied sources, a strategic yet difficult application. LSP is faster and more accurate than other existing high-quality methods, particularly where it was mostly tested, that is, for mapping text sets.

Axial T2 mapping in intervertebral discs: a new technique for assessment of intervertebral disc degeneration

To demonstrate the potential benefits of biochemical axial T2 mapping of intervertebral discs (IVDs) regarding the detection and grading of early stages of degenerative disc disease using 1.5-Tesla magnetic resonance imaging (MRI) in a clinical setting.

A systematic mapping study on testing technique experiments: has the situation changed since 2000?

Context: Empirical Software Engineering (ESE) replication researchers need to store and manipulate experimental data for several purposes, in particular analysis and reporting. Current research needs call for sharing and preservation of experimental data as well. In a previous work, we analyzed Replication Data Management (RDM) needs. A novel concept, called Experimental Ecosystem, was proposed to solve current deficiencies in RDM approaches. The empirical ecosystem provides replication researchers with a common framework that integrates transparently local heterogeneous data sources. A typical situation where the Empirical Ecosystem is applicable, is when several members of a research group, or several research groups collaborating together, need to share and access each other experimental results. However, to be able to apply the Empirical Ecosystem concept and deliver all promised benefits, it is necessary to analyze the software architectures and tools that can properly support it.