Pigment production by Streptococcus agalactiae in quasi-defined media.

A quasi-defined medium that supports the growth of Streptococcus agalactiae as pigmented colonies has been developed. The medium contains starch, a peptic digest of albumin, amino acids, nucleosides, vitamins, and salts. The presence of free cysteine, which could be replaced with other sulphur-containing compounds and to a lesser degree by reducing agents, was required for pigment formation.

A parameterization method for the computation of invariant tori and their whiskers in quasi-periodic maps: explorations and mechanisms for the breakdown of hyperbolicity

In two previous papers [J. Differential Equations, 228 (2006), pp. 530 579; Discrete Contin. Dyn. Syst. Ser. B, 6 (2006), pp. 1261 1300] we have developed fast algorithms for the computations of invariant tori in quasi‐periodic systems and developed theorems that assess their accuracy. In this paper, we study the results of implementing these algorithms and study their performance in actual implementations. More importantly, we note that, due to the speed of the algorithms and the theoretical developments about their reliability, we can compute with confidence invariant objects close to the breakdown of their hyperbolicity properties. This allows us to identify a mechanism of loss of hyperbolicity and measure some of its quantitative regularities. We find that some systems lose hyperbolicity because the stable and unstable bundles approach each other but the Lyapunov multipliers remain away from 1. We find empirically that, close to the breakdown, the distances between the invariant bundles and the Lyapunov multipliers which are natural measures of hyperbolicity depend on the parameters, with power laws with universal exponents. We also observe that, even if the rigorous justifications in [J. Differential Equations, 228 (2006), pp. 530-579] are developed only for hyperbolic tori, the algorithms work also for elliptic tori in Hamiltonian systems. We can continue these tori and also compute some bifurcations at resonance which may lead to the existence of hyperbolic tori with nonorientable bundles. We compute manifolds tangent to nonorientable bundles.

Tarification logit dans un réseau

Le problème de tarification qui nous intéresse ici consiste à maximiser le revenu généré par les usagers d'un réseau de transport. Pour se rendre à leurs destinations, les usagers font un choix de route et utilisent des arcs sur lesquels nous imposons des tarifs. Chaque route est caractérisée (aux yeux de l'usager) par sa "désutilité", une mesure de longueur généralisée tenant compte à la fois des tarifs et des autres coûts associés à son utilisation. Ce problème a surtout été abordé sous une modélisation déterministe de la demande selon laquelle seules des routes de désutilité minimale se voient attribuer une mesure positive de flot. Le modèle déterministe se prête bien à une résolution globale, mais pèche par manque de réalisme. Nous considérons ici une extension probabiliste de ce modèle, selon laquelle les usagers d'un réseau sont alloués aux routes d'après un modèle de choix discret logit. Bien que le problème de tarification qui en résulte est non linéaire et non convexe, il conserve néanmoins une forte composante combinatoire que nous exploitons à des fins algorithmiques. Notre contribution se répartit en trois articles. Dans le premier, nous abordons le problème d'un point de vue théorique pour le cas avec une paire origine-destination. Nous développons une analyse de premier ordre qui exploite les propriétés analytiques de l'affectation logit et démontrons la validité de règles de simplification de la topologie du réseau qui permettent de réduire la dimension du problème sans en modifier la solution. Nous établissons ensuite l'unimodalité du problème pour une vaste gamme de topologies et nous généralisons certains de nos résultats au problème de la tarification d'une ligne de produits. Dans le deuxième article, nous abordons le problème d'un point de vue numérique pour le cas avec plusieurs paires origine-destination. Nous développons des algorithmes qui exploitent l'information locale et la parenté des formulations probabilistes et déterministes. Un des résultats de notre analyse est l'obtention de bornes sur l'erreur commise par les modèles combinatoires dans l'approximation du revenu logit. Nos essais numériques montrent qu'une approximation combinatoire rudimentaire permet souvent d'identifier des solutions quasi-optimales. Dans le troisième article, nous considérons l'extension du problème à une demande hétérogène. L'affectation de la demande y est donnée par un modèle de choix discret logit mixte où la sensibilité au prix d'un usager est aléatoire. Sous cette modélisation, l'expression du revenu n'est pas analytique et ne peut être évaluée de façon exacte. Cependant, nous démontrons que l'utilisation d'approximations non linéaires et combinatoires permet d'identifier des solutions quasi-optimales. Finalement, nous en profitons pour illustrer la richesse du modèle, par le biais d'une interprétation économique, et examinons plus particulièrement la contribution au revenu des différents groupes d'usagers.

Transformations quasi-conformes de maillages volumiques et applications en infographie

La modélisation géométrique est importante autant en infographie qu'en ingénierie. Notre capacité à représenter l'information géométrique fixe les limites et la facilité avec laquelle on manipule les objets 3D. Une de ces représentations géométriques est le maillage volumique, formé de polyèdres assemblés de sorte à approcher une forme désirée. Certaines applications, tels que le placage de textures et le remaillage, ont avantage à déformer le maillage vers un domaine plus régulier pour faciliter le traitement. On dit qu'une déformation est \emph{quasi-conforme} si elle borne la distorsion. Cette thèse porte sur l’étude et le développement d'algorithmes de déformation quasi-conforme de maillages volumiques. Nous étudions ces types de déformations parce qu’elles offrent de bonnes propriétés de préservation de l’aspect local d’un solide et qu’elles ont été peu étudiées dans le contexte de l’informatique graphique, contrairement à leurs pendants 2D. Cette recherche tente de généraliser aux volumes des concepts bien maitrisés pour la déformation de surfaces. Premièrement, nous présentons une approche linéaire de la quasi-conformité. Nous développons une méthode déformant l’objet vers son domaine paramétrique par une méthode des moindres carrés linéaires. Cette méthode est simple d'implémentation et rapide d'exécution, mais n'est qu'une approximation de la quasi-conformité car elle ne borne pas la distorsion. Deuxièmement, nous remédions à ce problème par une approche non linéaire basée sur les positions des sommets. Nous développons une technique déformant le domaine paramétrique vers le solide par une méthode des moindres carrés non linéaires. La non-linéarité permet l’inclusion de contraintes garantissant l’injectivité de la déformation. De plus, la déformation du domaine paramétrique au lieu de l’objet lui-même permet l’utilisation de domaines plus généraux. Troisièmement, nous présentons une approche non linéaire basée sur les angles dièdres. Cette méthode définit la déformation du solide par les angles dièdres au lieu des positions des sommets du maillage. Ce changement de variables permet une expression naturelle des bornes de distorsion de la déformation. Nous présentons quelques applications de cette nouvelle approche dont la paramétrisation, l'interpolation, l'optimisation et la compression de maillages tétraédriques.

Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Perturbed Rankine vortices in surface quasi-geostrophic dynamics

An analytical dispersion relation is derived for linear perturbations to a Rankine vortex governed by surface quasi-geostrophic dynamics. Such a Rankine vortex is a circular region of uniform anomalous surface temperature evolving under quasi-geostrophic dynamics with uniform interior potential vorticity. The dispersion relation is analysed in detail and compared to the more familiar dispersion relation for a perturbed Rankine vortex governed by the Euler equations. The results are successfully verified against numerical simulations of the full equations. The dispersion relation is relevant to problems including wave propagation on surface temperature fronts and the stability of vortices in quasi-geostrophic turbulence.

EXACT AND QUASI-EXACT MODELS OF STRANGE STARS

We construct and compare in this work a variety of simple models for strange stars, namely, hypothetical self-bound objects made of a cold stable version of the quark-gluon plasma. Exact, quasi-exact and numerical models are examined to find the most economical description for these objects. A simple and successful parametrization of them is given in terms of the central density, and the differences among the models are explicitly shown and discussed. In particular, we present a model starting with a Gaussian ansatz for the density profile that provides a very accurate and almost complete analytical integration of the problem, modulo a small difference for one of the metric potentials.

Quasi-perfect state transfer in a bosonic dissipative network

In this paper we propose a scheme for quasi-perfect state transfer in a network of dissipative harmonic oscillators. We consider ideal sender and receiver oscillators connected by a chain of nonideal transmitter oscillators coupled by nearest-neighbour resonances. From the algebraic properties of the dynamical quantities describing the evolution of the network state, we derive a criterion, fixing the coupling strengths between all the oscillators, apart from their natural frequencies, enabling perfect state transfer in the particular case of ideal transmitter oscillators. Our criterion provides an easily manipulated formula enabling perfect state transfer in the special case where the network nonidealities are disregarded. We also extend such a criterion to dissipative networks where the fidelity of the transferred state decreases due to the loss mechanisms. To circumvent almost completely the adverse effect of decoherence, we propose a protocol to achieve quasi-perfect state transfer in nonideal networks. By adjusting the common frequency of the sender and the receiver oscillators to be out of resonance with that of the transmitters, we demonstrate that the sender`s state tunnels to the receiver oscillator by virtually exciting the nonideal transmitter chain. This virtual process makes negligible the decay rate associated with the transmitter line at the expense of delaying the time interval for the state transfer process. Apart from our analytical results, numerical computations are presented to illustrate our protocol.

Structured minimal-memory inexact quasi-Newton method and secant preconditioners for augmented Lagrangian optimization

Augmented Lagrangian methods for large-scale optimization usually require efficient algorithms for minimization with box constraints. On the other hand, active-set box-constraint methods employ unconstrained optimization algorithms for minimization inside the faces of the box. Several approaches may be employed for computing internal search directions in the large-scale case. In this paper a minimal-memory quasi-Newton approach with secant preconditioners is proposed, taking into account the structure of Augmented Lagrangians that come from the popular Powell-Hestenes-Rockafellar scheme. A combined algorithm, that uses the quasi-Newton formula or a truncated-Newton procedure, depending on the presence of active constraints in the penalty-Lagrangian function, is also suggested. Numerical experiments using the Cute collection are presented.

Dissipation-managed soliton in a quasi-one-dimensional Bose-Einstein condensate

We use the time-dependent mean-field Cross-Pitaevskii equation to study the formation of a dynamically-stabilized dissipation managed bright soliton in a quasi-one dimensional Bose-Einstein condensate (BEC). Because of three-body recombination of bosonic atoms to molecules, atoms are lost (dissipated) from a BEC. Such dissipation leads to the decay of a BEC soliton. We demonstrate by a perturbation procedure that an alimentation of atoms from an external source to the BEC may compensate for the dissipation loss and lead to a dynamically-stabilized soliton. The result of the analytical perturbation method is in excellent agreement with mean-field numerics. It seems possible to obtain such a dynamically stabilized BEC soliton without dissipation in laboratory.

Nonperturbative approach to potentials in impenetrable boxes based on quasi-exact solvability

In this work we develop an approach to obtain analytical expressions for potentials in an impenetrable box. In this kind of system the expression has the advantage of being valid for arbitrary values of the box length, and respect the correct quantum limits. The similarity of this kind of problem with the quasi exactly solvable potentials is explored in order to accomplish our goals. Problems related to the break of symmetries and simultaneous eigenfunctions of commuting operators are discussed.

Band-edge states of the zero(th)-order gap in quasi-periodic photonic superlattices

The photonic modes of Thue-Morse and Fibonacci lattices with generating layers A and B, of positive and negative indices of refraction, are calculated by the transfer-matrix technique. For Thue-Morse lattices, as well for periodic lattices with AB unit cell, the constructive interference of reflected waves, corresponding to the zero(th)-order gap, takes place when the optical paths in single layers A and B are commensurate. In contrast, for Fibonacci lattices of high order, the same phenomenon occurs when the ratio of those optical paths is close to the golden ratio. In the long wavelength limit, analytical expressions defining the edge frequencies of the zero(th) order gap are obtained for both quasi-periodic lattices. Furthermore, analytical expressions that define the gap edges around the zero(th) order gap are shown to correspond to the = 0 and = 0 conditions.

The dynamics of bright matter wave solitons in a quasi one-dimensional Bose-Einstein condensate with a rapidly varying trap

The dynamics of a bright matter wave soliton in a quasi one-dimensional Bose-Einstein condensate (BEC) with a periodically rapidly varying time trap is considered. The governing equation is based on averaging the fast modulations of the Gross-Pitaevskii (GP) equation. This equation has the form of a GP equation with an effective potential of a more complicated structure than an unperturbed trap. In the case of an inverted (expulsive) quadratic trap corresponding to an unstable GP equation, the effective potential can be stable. For the bounded space trap potential it is showed that bifurcation exists, i.e. the single-well potential bifurcates to the triple-well effective potential. The stabilization of a BEC cloud on-site state in the temporary modulated optical lattice is found. This phenomenon is analogous to the Kapitza stabilization of an inverted pendulum. The analytical predictions of the averaged GP equation are confirmed by numerical simulations of the full GP equation with rapid perturbations.

Modelagem numérica da influência do eletrojato equatorial em dados magnetotelúricos produzidos por estruturas tridimensionais

A América do Sul apresenta várias peculiaridades geomagnéticas, uma delas, é a presença do Eletrojato Equatorial, o qual se estende de leste para oeste no Brasil ao longo de aproximadamente 3500 km. Considerando-se o fato de que a influência do Eletrojato Equatorial pode ser detectada a grandes distâncias do seu centro, isto suscita o interesse em se estudar os seus efeitos na exploração magnetotelúrica no Brasil. A influência do eletrojato equatorial na prospecção magnetotelúrica tem sido modelada para meios geológicos uni e bidimensionais valendo-se para isto de soluções analíticas fechadas e de técnicas numéricas tais como elementos finitos e diferenças finitas. Em relação aos meios geológicos tridimensionais, eles tem sido modelados na forma de "camadas finas", usando o algoritmo "thin sheet". As fontes indutoras utilizadas para simular o eletrojato equatorial nestes trabalhos, tem sido linhas de corrente, eletrojatos gaussianos e eletrojatos ondulantes. Por outro lado, o objetivo principal da nossa tese foi o modelamento dos efeitos que o eletrojato equatorial provoca em estruturas tridimensionais próprias da geofísica da prospecção. Com tal finalidade, utilizamos o esquema numérico da equação integral, com as fontes indutoras antes mencionadas. De maneira similar aos trabalhos anteriores, os nossos resultados mostram que a influência do eletrojato equatorial somente acontece em frequências menores que 10^-1 Hz. Este efeito decresce com a distância, mantendo-se até uns 3000 km do centro do eletrojato. Assim sendo, a presença de grandes picos nos perfis da resistividade aparente de um semi-espaço homogêneo, indica que a influência do eletrojato é notável neste tipo de meio. Estes picos se mostram com diferente magnitude para cada eletrojato simulado, sendo que a sua localização também muda de um eletrojato para outro. Entretanto, quando se utilizam modelos geo-elétricos unidimensionais mais de acordo com a realidade, tais como os meios estratificados, percebe-se que a resposta dos eletrojatos se amortece significativamente e não mostra muitas diferenças entre os diferentes tipos de eletrojato. Isto acontece por causa da dissipação da energia eletromagnética devido à presença da estratificação e de camadas condutivas. Dentro do intervalo de 3000 km, a resposta eletromagnética tridimensional pode ser deslocada para cima ou para baixo da resposta da onda plana, dependendo da localização do corpo, da frequência, do tipo de eletrojato e do meio geológico. Quando a resposta aparece deslocada para cima, existe um afastamento entre as sondagens uni e tridimensionais devidas ao eletrojato, assim como um alargamento da anomalia dos perfis que registra a presença da heterogeneidade tridimensional. Quando a resposta aparece deslocada para baixo, no entanto, há uma aproximação entre estes dois tipos de sondagens e um estreitamento da anomalia dos perfis. Por outro lado, a fase se mostra geralmente, de uma forma invertida em relação à resistividade aparente. Isto significa que quando uma sobe a outra desce, e vice-versa. Da mesma forma, comumente nas altas frequências as respostas uni e tridimensionais aparecem deslocadas, enquanto que nas baixas frequências se mostram com os mesmos valores, com exceção dos eletrojatos ondulantes com parâmetros de ondulação α = —2 e —3. Nossos resultados também mostram que características geométricas próprias das estruturas tridimensionais, tais como sua orientação em relação à direção do eletrojato e a dimensão da sua direção principal, afetam a resposta devido ao eletrojato em comparação com os resultados da onda plana. Desta forma, quando a estrutura tridimensional é rotacionada de 90°, em relação à direção do eletrojato e em torno do eixo z, existe uma troca de polarizações nas resistividades dos resultados, mas não existem mudanças nos valores da resistividade aparente no centro da estrutura. Ao redor da mesma, porém, se percebe facilmente alterações nos contornos dos mapas de resistividade aparente, ao serem comparadas com os mapas da estrutura na sua posição original. Isto se deve à persistência dos efeitos galvânicos no centro da estrutura e à presença de efeitos indutivos ao redor do corpo tridimensional. Ao alongar a direção principal da estrutura tridimensional, as sondagens magnetotelúricas vão se aproximando das sondagens das estruturas bidimensionais, principalmente na polarização XY. Mesmo assim, as respostas dos modelos testados estão muito longe de se considerar próximas das respostas de estruturas quase-bidimensionais. Porém, os efeitos do eletrojato em estruturas com direção principal alongada, são muito parecidos com aqueles presentes nas estruturas menores, considerando-se as diferenças entre as sondagens de ambos tipos de estruturas. Por outro lado, os mapas de resistividade aparente deste tipo de estrutura alongada, revelam um grande aumento nos extremos da estrutura, tanto para a onda plana como para o eletrojato. Este efeito é causado pelo acanalamento das correntes ao longo da direção principal da estrutura. O modelamento de estruturas geológicas da Bacia de Marajó confirma que os efeitos do eletrojato podem ser detetados em estruturas pequenas do tipo "horst" ou "graben", a grandes distâncias do centro do mesmo. Assim, os efeitos do eletrojato podem ser percebidos tanto nos meios estratificados como tridimensionais, em duas faixas de freqüência (nas proximidades de 10^-1 Hz e para freqüências menores que 10^-3 Hz), possivelmente influenciados pela presença do embasamento cristalino e a crosta inferior, respectivamente. Desta maneira, os resultados utilizando o eletrojato como fonte indutora, mostram que nas baixas freqüências as sondagens magnetotelúricas podem ser fortemente distorcidas, tanto pelos efeitos galvânicos da estrutura tridimensional como pela presença da influência do eletrojato. Conseqüêntemente, interpretações errôneas dos dados de campo podem ser cometidas, se não se corrigirem os efeitos do eletrojato equatorial ou, da mesma forma, não se utilisarem algoritmos tridimensionais para interpretar os dados, no lugar do usual modelo unidimensional de Tikhonov - Cagniard.

An Analytical Model for Virtual Topology Reconfiguration in Optical Networks and A Case Study

An analytical model for Virtual Topology Reconfiguration (VTR) in optical networks is developed. It aims at the optical networks with a circuit-based data plane and an IPlike control plane. By identifying and analyzing the important factors impacting the network performance due to VTR operations on both planes, we can compare the benefits and penalties of different VTR algorithms and policies. The best VTR scenario can be adaptively chosen from a set of such algorithms and policies according to the real-time network situations. For this purpose, a cost model integrating all these factors is created to provide a comparison criterion independent of any specific VTR algorithm and policy. A case study based on simulation experiments is conducted to illustrate the application of our models.