Une signature du polymorphisme structural d’acides ribonucléiques non-codants permettant de comparer leurs niveaux d’activités biochimiques

Des évidences expérimentales récentes indiquent que les ARN changent de structures au fil du temps, parfois très rapidement, et que ces changements sont nécessaires à leurs activités biochimiques. La structure de ces ARN est donc dynamique. Ces mêmes évidences notent également que les structures clés impliquées sont prédites par le logiciel de prédiction de structure secondaire MC-Fold. En comparant les prédictions de structures du logiciel MC-Fold, nous avons constaté un lien clair entre les structures presque optimales (en termes de stabilité prédites par ce logiciel) et les variations d’activités biochimiques conséquentes à des changements ponctuels dans la séquence. Nous avons comparé les séquences d’ARN du point de vue de leurs structures dynamiques afin d’investiguer la similarité de leurs fonctions biologiques. Ceci a nécessité une accélération notable du logiciel MC-Fold. L’approche algorithmique est décrite au chapitre 1. Au chapitre 2 nous classons les impacts de légères variations de séquences des microARN sur la fonction naturelle de ceux-ci. Au chapitre 3 nous identifions des fenêtres dans de longs ARN dont les structures dynamiques occupent possiblement des rôles dans les désordres du spectre autistique et dans la polarisation des œufs de certains batraciens (Xenopus spp.).

Analysis and Optimization of Machining Process Using Evolutionary Algorithms

To ensure quality of machined products at minimum machining costs and maximum machining effectiveness, it is very important to select optimum parameters when metal cutting machine tools are employed. Traditionally, the experience of the operator plays a major role in the selection of optimum metal cutting conditions. However, attaining optimum values each time by even a skilled operator is difficult. The non-linear nature of the machining process has compelled engineers to search for more effective methods to attain optimization. The design objective preceding most engineering design activities is simply to minimize the cost of production or to maximize the production efficiency. The main aim of research work reported here is to build robust optimization algorithms by exploiting ideas that nature has to offer from its backyard and using it to solve real world optimization problems in manufacturing processes.In this thesis, after conducting an exhaustive literature review, several optimization techniques used in various manufacturing processes have been identified. The selection of optimal cutting parameters, like depth of cut, feed and speed is a very important issue for every machining process. Experiments have been designed using Taguchi technique and dry turning of SS420 has been performed on Kirlosker turn master 35 lathe. Analysis using S/N and ANOVA were performed to find the optimum level and percentage of contribution of each parameter. By using S/N analysis the optimum machining parameters from the experimentation is obtained.Optimization algorithms begin with one or more design solutions supplied by the user and then iteratively check new design solutions, relative search spaces in order to achieve the true optimum solution. A mathematical model has been developed using response surface analysis for surface roughness and the model was validated using published results from literature.Methodologies in optimization such as Simulated annealing (SA), Particle Swarm Optimization (PSO), Conventional Genetic Algorithm (CGA) and Improved Genetic Algorithm (IGA) are applied to optimize machining parameters while dry turning of SS420 material. All the above algorithms were tested for their efficiency, robustness and accuracy and observe how they often outperform conventional optimization method applied to difficult real world problems. The SA, PSO, CGA and IGA codes were developed using MATLAB. For each evolutionary algorithmic method, optimum cutting conditions are provided to achieve better surface finish.The computational results using SA clearly demonstrated that the proposed solution procedure is quite capable in solving such complicated problems effectively and efficiently. Particle Swarm Optimization (PSO) is a relatively recent heuristic search method whose mechanics are inspired by the swarming or collaborative behavior of biological populations. From the results it has been observed that PSO provides better results and also more computationally efficient.Based on the results obtained using CGA and IGA for the optimization of machining process, the proposed IGA provides better results than the conventional GA. The improved genetic algorithm incorporating a stochastic crossover technique and an artificial initial population scheme is developed to provide a faster search mechanism. Finally, a comparison among these algorithms were made for the specific example of dry turning of SS 420 material and arriving at optimum machining parameters of feed, cutting speed, depth of cut and tool nose radius for minimum surface roughness as the criterion. To summarize, the research work fills in conspicuous gaps between research prototypes and industry requirements, by simulating evolutionary procedures seen in nature that optimize its own systems.

Stochastic Inventory with/without Service Time, Reneging and Retrial of Customers

This thesis Entitled Stochastic modelling and analysis.This thesis is divided into six chapters including this introductory chapter. In second chapter, we consider an (s,S) inventory model with service, reneging of customers and finite shortage of items.In the third chapter, we consider an (s,S) inventoiy system with retrial of customers. Arrival of customers forms a Poisson process with rate. When the inventory level depletes to s due to demands, an order for replenishment is placed.In Chapter 4, we analyze and compare three (s,S) inventory systems with positive service time and retrial of customers. In all these systems, arrivals of customers form a Poisson process and service times are exponentially distributed. In chapter 5, we analyze and compare three production inventory systems with positive service time and retrial of customers. In all these systems, arrivals of customers form a Poisson process and service times are exponentially distributed.In chapter 6, we consider a PH /PH /l inventory model with reneging of customers and finite shortage of items.

Palladium Catalyzed Carbon-Carbon/Carbonheteroatom Bond Formation Reactions Utilizing Pentafulvene Derived Bicyclic Hydrazines

The reactions involving fulvenes and its derivatives have received a great deal of attention over the years in synthetic organic chemistry. Functionalizations of fulvenes provide versatile and powerful approaches to various polycyclic systems and natural products. They serve as versatile intermediates in the construction of various ring systems through inter- as well as intramolecular cycloadditions. Compared to the rich literature on the cycloaddition reactions of pentafulvenes, much less attention has been paid to the synthetic utilization of their cycloadducts. Tactical manipulations on the chosen adduct offer the prospects for designing a variety of useful molecular skeletons. Addition of heterodienophiles to fulvenes offers an efficient strategy towards the synthesis of azabicyclic olefins. However, there have been no serious attempts to study the synthetic utility of these substrates. In this context and with the intention of utilizing pentafulvenes towards synthetically important molecules, author decided to explore the reactivity of pentafulvene derived azabicyclic olefins. Our attention was focused on the synthetic potential associated with the ring opening of fulvene derived bicyclic hydrazines under palladium catalysis. It was envisioned that the desymmetrization of these adducts using various soft nucleophiles will provide a novel access to synthetically and biologically important alkylidene cyclopentenes. The investigations along this line form the focal theme of this thesis entitled “PALLADIUM CATALYZED CARBONCARBON/ CARBON-HETEROATOM BOND FORMATION REACTIONS UTILIZING PENTAFULVENE DERIVED BICYCLIC HYDRAZINES

Developing a Child Friendly Text-to-Speech System

This paper discusses the implementation details of a child friendly, good quality, English text-to-speech (TTS) system that is phoneme-based, concatenative, easy to set up and use with little memory. Direct waveform concatenation and linear prediction coding (LPC) are used. Most existing TTS systems are unit-selection based, which use standard speech databases available in neutral adult voices.Here reduced memory is achieved by the concatenation of phonemes and by replacing phonetic wave files with their LPC coefficients. Linguistic analysis was used to reduce the algorithmic complexity instead of signal processing techniques. Sufficient degree of customization and generalization catering to the needs of the child user had been included through the provision for vocabulary and voice selection to suit the requisites of the child. Prosody had also been incorporated. This inexpensive TTS systemwas implemented inMATLAB, with the synthesis presented by means of a graphical user interface (GUI), thus making it child friendly. This can be used not only as an interesting language learning aid for the normal child but it also serves as a speech aid to the vocally disabled child. The quality of the synthesized speech was evaluated using the mean opinion score (MOS).

Evaluating the state of the art of parallel programming systems

This paper describes our plans to evaluate the present state of affairs concerning parallel programming and its systems. Three subprojects are proposed: a survey among programmers and scientists, a comparison of parallel programming systems using a standard set of test programs, and a wiki resource for the parallel programming community - the Parawiki. We would like to invite you to participate and turn these subprojects into true community efforts.

Computation of locally free class groups

We show that the locally free class group of an order in a semisimple algebra over a number field is isomorphic to a certain ray class group. This description is then used to present an algorithm that computes the locally free class group. The algorithm is implemented in MAGMA for the case where the algebra is a group ring over the rational numbers.

Exact algorithms for p-adic fields and epsilon constant conjectures

We develop several algorithms for computations in Galois extensions of p-adic fields. Our algorithms are based on existing algorithms for number fields and are exact in the sense that we do not need to consider approximations to p-adic numbers. As an application we describe an algorithmic approach to prove or disprove various conjectures for local and global epsilon constants.

Collaborative design procedures for architects and engineers

This book argues for novel strategies to integrate engineering design procedures and structural analysis data into architectural design. Algorithmic procedures that recently migrated into the architectural practice are utilized to improve the interface of both disciplines. Architectural design is predominately conducted as a negotiation process of various factors but often lacks rigor and data structures to link it to quantitative procedures. Numerical structural design on the other hand could act as a role model for handling data and robust optimization but it often lacks the complexity of architectural design. The goal of this research is to bring together robust methods from structural design and complex dependency networks from architectural design processes. The book presents three case studies of tools and methods that are developed to exemplify, analyze and evaluate a collaborative work flow.

On CD-systems of stateless deterministic R-automata with window size one

We study cooperating distributed systems (CD-systems) of restarting automata that are very restricted: they are deterministic, they cannot rewrite, but only delete symbols, they restart immediately after performing a delete operation, they are stateless, and they have a read/write window of size 1 only, that is, these are stateless deterministic R(1)-automata. We study the expressive power of these systems by relating the class of languages that they accept by mode =1 computations to other well-studied language classes, showing in particular that this class only contains semi-linear languages, and that it includes all rational trace languages. In addition, we investigate the closure and non-closure properties of this class of languages and some of its algorithmic properties.

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.

On Connection, Linearization and Duplication Coefficients of Classical Orthogonal Polynomials

In this work, we have mainly achieved the following: 1. we provide a review of the main methods used for the computation of the connection and linearization coefficients between orthogonal polynomials of a continuous variable, moreover using a new approach, the duplication problem of these polynomial families is solved; 2. we review the main methods used for the computation of the connection and linearization coefficients of orthogonal polynomials of a discrete variable, we solve the duplication and linearization problem of all orthogonal polynomials of a discrete variable; 3. we propose a method to generate the connection, linearization and duplication coefficients for q-orthogonal polynomials; 4. we propose a unified method to obtain these coefficients in a generic way for orthogonal polynomials on quadratic and q-quadratic lattices. Our algorithmic approach to compute linearization, connection and duplication coefficients is based on the one used by Koepf and Schmersau and on the NaViMa algorithm. Our main technique is to use explicit formulas for structural identities of classical orthogonal polynomial systems. We find our results by an application of computer algebra. The major algorithmic tools for our development are Zeilberger’s algorithm, q-Zeilberger’s algorithm, the Petkovšek-van-Hoeij algorithm, the q-Petkovšek-van-Hoeij algorithm, and Algorithm 2.2, p. 20 of Koepf's book "Hypergeometric Summation" and it q-analogue.

Elimination in Operator Algebras

A large class of special functions are solutions of systems of linear difference and differential equations with polynomial coefficients. For a given function, these equations considered as operator polynomials generate a left ideal in a noncommutative algebra called Ore algebra. This ideal with finitely many conditions characterizes the function uniquely so that Gröbner basis techniques can be applied. Many problems related to special functions which can be described by such ideals can be solved by performing elimination of appropriate noncommutative variables in these ideals. In this work, we mainly achieve the following: 1. We give an overview of the theoretical algebraic background as well as the algorithmic aspects of different methods using noncommutative Gröbner elimination techniques in Ore algebras in order to solve problems related to special functions. 2. We describe in detail algorithms which are based on Gröbner elimination techniques and perform the creative telescoping method for sums and integrals of special functions. 3. We investigate and compare these algorithms by illustrative examples which are performed by the computer algebra system Maple. This investigation has the objective to test how far noncommutative Gröbner elimination techniques may be efficiently applied to perform creative telescoping.

Formal Multilevel Hierarchical Verification of Synchronous MOS Circuits

I have designed and implemented a system for the multilevel verification of synchronous MOS VLSI circuits. The system, called Silica Pithecus, accepts the schematic of an MOS circuit and a specification of the circuit's intended digital behavior. Silica Pithecus determines if the circuit meets its specification. If the circuit fails to meet its specification Silica Pithecus returns to the designer the reason for the failure. Unlike earlier verifiers which modelled primitives (e.g., transistors) as unidirectional digital devices, Silica Pithecus models primitives more realistically. Transistors are modelled as bidirectional devices of varying resistances, and nodes are modelled as capacitors. Silica Pithecus operates hierarchically, interactively, and incrementally. Major contributions of this research include a formal understanding of the relationship between different behavioral descriptions (e.g., signal, boolean, and arithmetic descriptions) of the same device, and a formalization of the relationship between the structure, behavior, and context of device. Given these formal structures my methods find sufficient conditions on the inputs of circuits which guarantee the correct operation of the circuit in the desired descriptive domain. These methods are algorithmic and complete. They also handle complex phenomena such as races and charge sharing. Informal notions such as races and hazards are shown to be derivable from the correctness conditions used by my methods.

Sequences and Modules

This is a presentation introducing students to algorithmic concepts such as sequencing, pseudocode and modularity. It includes a class exercise to define the algorithm to make a cup of tea.