Semi-algebraic methods for symbolic analysis of complex reaction networks

The identification of chemical mechanism that can exhibit oscillatory phenomena in reaction networks are currently of intense interest. In particular, the parametric question of the existence of Hopf bifurcations has gained increasing popularity due to its relation to the oscillatory behavior around the fixed points. However, the detection of oscillations in high-dimensional systems and systems with constraints by the available symbolic methods has proven to be difficult. The development of new efficient methods are therefore required to tackle the complexity caused by the high-dimensionality and non-linearity of these systems. In this thesis, we mainly present efficient algorithmic methods to detect Hopf bifurcation fixed points in (bio)-chemical reaction networks with symbolic rate constants, thereby yielding information about their oscillatory behavior of the networks. The methods use the representations of the systems on convex coordinates that arise from stoichiometric network analysis. One of the methods called HoCoQ reduces the problem of determining the existence of Hopf bifurcation fixed points to a first-order formula over the ordered field of the reals that can then be solved using computational-logic packages. The second method called HoCaT uses ideas from tropical geometry to formulate a more efficient method that is incomplete in theory but worked very well for the attempted high-dimensional models involving more than 20 chemical species. The instability of reaction networks may lead to the oscillatory behaviour. Therefore, we investigate some criterions for their stability using convex coordinates and quantifier elimination techniques. We also study Muldowney's extension of the classical Bendixson-Dulac criterion for excluding periodic orbits to higher dimensions for polynomial vector fields and we discuss the use of simple conservation constraints and the use of parametric constraints for describing simple convex polytopes on which periodic orbits can be excluded by Muldowney's criteria. All developed algorithms have been integrated into a common software framework called PoCaB (platform to explore bio- chemical reaction networks by algebraic methods) allowing for automated computation workflows from the problem descriptions. PoCaB also contains a database for the algebraic entities computed from the models of chemical reaction networks.

Meshing highly regular structures: The case of super carbon nanotubes of arbitrary order

Mesh generation is an important step inmany numerical methods.We present the “HierarchicalGraphMeshing” (HGM)method as a novel approach to mesh generation, based on algebraic graph theory.The HGM method can be used to systematically construct configurations exhibiting multiple hierarchies and complex symmetry characteristics. The hierarchical description of structures provided by the HGM method can be exploited to increase the efficiency of multiscale and multigrid methods. In this paper, the HGMmethod is employed for the systematic construction of super carbon nanotubes of arbitrary order, which present a pertinent example of structurally and geometrically complex, yet highly regular, structures. The HGMalgorithm is computationally efficient and exhibits good scaling characteristics. In particular, it scales linearly for super carbon nanotube structures and is working much faster than geometry-based methods employing neighborhood search algorithms. Its modular character makes it conducive to automatization. For the generation of a mesh, the information about the geometry of the structure in a given configuration is added in a way that relates geometric symmetries to structural symmetries. The intrinsically hierarchic description of the resulting mesh greatly reduces the effort of determining mesh hierarchies for multigrid and multiscale applications and helps to exploit symmetry-related methods in the mechanical analysis of complex structures.

Internal Camera Calibration Using Rotation and Geometric Shapes

This paper describes a simple method for internal camera calibration for computer vision. This method is based on tracking image features through a sequence of images while the camera undergoes pure rotation. The location of the features relative to the camera or to each other need not be known and therefore this method can be used both for laboratory calibration and for self calibration in autonomous robots working in unstructured environments. A second method of calibration is also presented. This method uses simple geometric objects such as spheres and straight lines to The camera parameters. Calibration is performed using both methods and the results compared.

Image Based Rendering Using Algebraic Techniques

This paper presents an image-based rendering system using algebraic relations between different views of an object. The system uses pictures of an object taken from known positions. Given three such images it can generate "virtual'' ones as the object would look from any position near the ones that the two input images were taken from. The extrapolation from the example images can be up to about 60 degrees of rotation. The system is based on the trilinear constraints that bind any three view so fan object. As a side result, we propose two new methods for camera calibration. We developed and used one of them. We implemented the system and tested it on real images of objects and faces. We also show experimentally that even when only two images taken from unknown positions are given, the system can be used to render the object from other view points as long as we have a good estimate of the internal parameters of the camera used and we are able to find good correspondence between the example images. In addition, we present the relation between these algebraic constraints and a factorization method for shape and motion estimation. As a result we propose a method for motion estimation in the special case of orthographic projection.

Geometric Structure of the Adaptive Controller of the Human Arm

The objects with which the hand interacts with may significantly change the dynamics of the arm. How does the brain adapt control of arm movements to this new dynamic? We show that adaptation is via composition of a model of the task's dynamics. By exploring generalization capabilities of this adaptation we infer some of the properties of the computational elements with which the brain formed this model: the elements have broad receptive fields and encode the learned dynamics as a map structured in an intrinsic coordinate system closely related to the geometry of the skeletomusculature. The low--level nature of these elements suggests that they may represent asset of primitives with which a movement is represented in the CNS.

Geometric Aspects of Visual Object Recognition

This thesis presents there important results in visual object recognition based on shape. (1) A new algorithm (RAST; Recognition by Adaptive Sudivisions of Tranformation space) is presented that has lower average-case complexity than any known recognition algorithm. (2) It is shown, both theoretically and empirically, that representing 3D objects as collections of 2D views (the "View-Based Approximation") is feasible and affects the reliability of 3D recognition systems no more than other commonly made approximations. (3) The problem of recognition in cluttered scenes is considered from a Bayesian perspective; the commonly-used "bounded-error errorsmeasure" is demonstrated to correspond to an independence assumption. It is shown that by modeling the statistical properties of real-scenes better, objects can be recognized more reliably.

Matlab Code for Modulators

Considers Sampling, Pulse Amplitude Modulation, Multiple Access, Quantisation, Pulse Coded Modulation, Manchester Line Coding, Amplitude Modulation, Double SideBand Suppressed Carrier Modulation, Quadrature Amplitude Modulation and M-ary Shift Keying.

Matlab Code for Entropy Coding

Considers Huffman coding and arithmetic coding

eHandbook-eFolio Module Import code

Code required to perform an import of module information from eFolio and output it into a single page. Within the context of eHandbook: this page is called via an iFrame to display module information as part of the handbook (and to avoid any duplication of content).

Safety information and dress code for practical sessions

This resource is for Health Scientists

COMP1205 LEPP: BCS Code of Conduct

Notes, slides, links

Geometric characterization of red blood cells. Differentiation of normal and pathologic samples

Introduction. Fractal geometry measures the irregularity of abstract and natural objects with the fractal dimension. Fractal calculations have been applied to the structures of the human body and to quantifications in physiology from the theory of dynamic systems.Material and Methods. The fractal dimensions were calculated, the number of occupation spaces in the space border of box counting and the area of two red blood cells groups, 7 normal ones, group A, and 7 abnormal, group B, coming from patient and of bags for transfusion, were calculated using the method of box counting and a software developed for such effect. The obtained measures were compared, looking for differences between normal and abnormal red blood cells, with the purpose of differentiating samples.Results. The abnormality characterizes by a number of squares of occupation of the fractal space greater or equal to 180; values of areas between 25.117 and 33.548 correspond to normality. In case that the evaluation according to the number of pictures is of normality, must be confirmed with the value of the area applied to adjacent red blood cells within the sample, that in case of having values by outside established and/or the greater or equal spaces to 180, they suggest abnormality of the sample.Conclusions. The developed methodology is effective to differentiate the red globules alterations and probably useful in the analysis of bags of transfusion for clinical use 

¿Puedo tener un code-switching? : codeswitching en estudiantes de doctorado enseñando cursos de español lengua extranjera.

Memoria de máster (Universidad de Texas, 2010). Resumen basado en el de la publicación

On the Development of Early Algebraic Thinking. 'Sobre el desarrollo del pensamiento algebraico temprano'.

Resumen basado en el de la publicación

"Au-delà du code civil mais par le code civil". Raymond Saleilles (1855-1912) y la lucha por el derecho comparado

Raymond Saleilles (1855-1912) és considerat pels comparatistes com pare del dret comparat modern. De fet fou el màxim responsable de l'organització del primer congrés internacional de dret comparat a París el 1900. L'època marcada per la internacionalització dels intercanvis, la crisi del mètode jurídic francès i el repte de la codificació alemanya i suïssa motivà alguns juristes a buscar noves formes d'estudiar el dret. Saleilles defensava pel dret comparat un mètode, un objecte i un fi propis i autònoms diferents dels que fins ara tenien la dogmàtica jurídica o l'estudi de la legislació estrangera. El mètode tenia els seus fonaments en la sociologia i la història. L'objectiu del dret comparat havia de ser la construcció d'un ideal "droit commun de l'humanité civilisée". Aquest dret comú havia de ser construït no només per la doctrina sinó també per la jurisprudència i el legislador.