Threading is a protein structure prediction method that uses a library of template protein structures in the following steps: first the target sequence is matched to the template library and the best template structure is selected, secondly the predicted target structure of the target sequence is modeled by this selected template structure. The deceleration of new folds which are added to the protein data bank promises completion of the template structure library. This thesis uses a new set of template-specific weights to improve the energy function for sequence-to-structure alignment in the template selection step of the threading process. The weights are estimated using least squares methods with the quality of the modelling step in the threading process as the label. These new weights show an average 12.74% improvement in estimating the label. Further family analysis show a correlation between the performance of the new weights to the number of seeds in pFam.

Threading is a protein structure prediction method that uses a library of template protein structures in the following steps: first the target sequence is matched to the template library and the best template structure is selected, secondly the predicted target structure of the target sequence is modeled by this selected template structure. The deceleration of new folds which are added to the protein data bank promises completion of the template structure library. This thesis uses a new set of template-specific weights to improve the energy function for sequence-to-structure alignment in the template selection step of the threading process. The weights are estimated using least squares methods with the quality of the modelling step in the threading process as the label. These new weights show an average 12.74% improvement in estimating the label. Further family analysis show a correlation between the performance of the new weights to the number of seeds in pFam.

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Communicating Sequential Processes (CSP) is a formal language whose primary purpose is to model and verify concurrent systems. The CSP++ toolset was created to embody the concept of selective formalism by making machine-readable CSPm specifications both executable (through the automatic synthesis of C++ source) and extensible (by allowing the integration of C++ user-coded functions). However, these user-coded functions were limited by their inability to share data with each other, which meant that their application was constrained to solving simple problems in isolation. We extend CSP++ by providing user-coded functions in the same CSP process with safe access to a shared storage area, similar in concept and API to Pthreads' thread-local storage, enabling cooperation between them and granting them the ability to undertake more complex tasks without breaking the formalism of the underlying specification. This feature's utility is demonstrated in our line-following robot case study.

This thesis represents an attempt to improve the state of the art in our ability tounderstand and check object protocols, with a particular emphasis on concurrent pro-grams. Object protocols are the patterns of use imposed on clients of APIs in object-oriented programs. We show through an empirical study of open-source object-oriented programs that object protocols are quite common. We then present “Sync-or-Swim,” a methodology and suite of accompanying tools for checking at compile-time that object protocols are used and implemented correctly. This methodology isbased upon the existing access permissions method of alias control, which is hereextended to be sound in the face of shared-memory concurrency. The analysis isformalized as a type system for an object-oriented calculus, and then proven to befree from false-negatives using a proof of type safety. The type system is extendedwith parametric polymorphism, or “generics,” in order to increase its ability to checkcommonly occurring patterns. An implementation of the approach, a static analysisfor programs written in the Java programming language, is presented. This imple-mentation was used to perform a series of case studies whose goal was to evaluatethe ease of use, expressiveness and ability to verify commonly occurring patterns.These case studies are presented. Next, an approach and an associated tool for in-ferring access permission annotations is presented. This inference tool can reducethe burden of using our protocol-checking approach by automatically inferring therequired typing annotations. This inference is built upon a system of probabilisticconstraints, which allows the easy encoding of heuristics. Finally, an optimization ofsoftware transactional memory runtimes is presented. This optimization is enabledby the typing annotations required to use the concurrent protocol checker and canremove some of the overhead typically associated with transactional memory sys-tems. As a result of the work presented in this thesis, it is possible to guarantee theabsence of certain API usage errors even in concurrent programs, and to do so witha low burden on programmers. By adhering to such an approach, programmers canproduce more reliable software.

DNA is the code for all life. Via intermediary RNA the information encoded by the genome is relayed to proteins executing the various functions in a cell. Together, this repertoire of inherently linked biological macromolecules determines all characteristics and features of a cell. Technological advancements during the last decades have enabled the pursuit of novel types of studies and the investigation of the cell and its constituents at a progressively higher level of detail. This has shed light on numerous cellular processes and on the underpinnings of several diseases. For the majority of studies focusing on nucleic acids, an amplification step has to be implemented before an analysis, scoring or interrogation method translates the amplified material into relevant biological information. This information can, for instance, be the genotype of particular SNPs or STRs, or the abundance level of a set of interesting transcripts. As such, amplification plays a significant role in nucleic acid assays. Over the years, a number of techniques – most notably PCR – has been devised to meet this amplification need, specifically or randomly multiplying desired regions. However, many of the approaches do not scale up easily rendering comprehensive studies cumbersome, time-consuming and necessitating large quantities of material.Trinucleotide threading (TnT) – forming the red thread throughout this thesis – is a multiplex amplification method, enabling simultaneous targeted amplification of several nucleic acid regions in a specific manner. TnT begins with a controlled linear DNA thread formation, each type of thread corresponding to a segment of interest, by a gap-fill reaction using a restricted trinucleotide set. The whole collection of created threads is subsequently subjected to an exponential PCR amplification employing a single primer pair. The generated material can thereafter be analyzed with a multitude of readout and detection platforms depending on the issue or characteristic under consideration.TnT offers a high level of specificity by harnessing the inherent specificities of a polymerase and a ligase acting on a nucleotide set encompassing three out of the four nucleotide types. Accordingly, several erroneous events have to occur in order to produce artifacts. This necessitates override of a number of control points.The studies constituting this thesis demonstrate integration of the TnT amplification strategy in assays for analysis of various aspects of DNA and RNA. TnT was adapted for expression profiling of intermediately-sized gene sets using both conventional DNA microarrays and massively parallel second generation 454 sequencing for readout. TnT, in conjunction with 454 sequencing, was also employed for allelotyping, defined as determination of allele frequencies in a cohort. In this study, 147 SNPs were simultaneously assayed in a pool comprising genomic DNA of 462 individuals. Finally, TnT was recruited for parallel amplification of STR loci with detection relying on capillary gel electrophoresis. In all investigations, the material generated with TnT was of sufficient quality and quantity to produce reliable and accurate biological information.Taken together, TnT represents a viable multiplex amplification technique permitting parallel amplification of genomic segments, for instance harboring polymorphisms, or of expressed genes. In addition to these, this versatile amplification module can be implemented in assays targeting a range of other features of genomes and transcriptomes. / QC 20100819

Made available in DSpace on 2014-12-17T14:58:24Z (GMT). No. of bitstreams: 1 IgorLA_DISSERT.pdf: 5014153 bytes, checksum: b4c50270935571b9e1c875a8c15841c3 (MD5) Previous issue date: 2014-02-26 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / In machining of internal threads, dedicated tools, known as taps, are needed for each profile type, diameter, and low cutting speed values are used when compared to main machining processes. This restriction in the cutting speed is associated with the difficulty of synchronizing the tool s rotation speed and feed velocity in the process. This fact restricts the flexibility and makes machining lead times longer when manufacturing of components with threads is required. An alternative to the constraints imposed by the tap is the thread milling with helical interpolation technique. The technique is the fusion of two movements: rotation and helical interpolation. The tools may have different configurations: a single edge or multiple edges (axial, radial or both). However, thread milling with helical interpolation technique is relatively new and there are limited studies on the subject, a fact which promotes challenges to its wide application in the manufacturing shop floor. The objective of this research is determine the performance of different types of tools in the thread milling with helical interpolation technique using hardened steel workpieces. In this sense, four tool configurations were used for threading milling in AISI 4340 quenched and tempered steel (40 HRC). The results showed that climb cut promoted a greater number of machined threads, regardless of tool configuration. The upcut milling causes chippings in cutting edge, while the climb cutting promotes abrasive wear. Another important point is that increase in hole diameter by tool diameter ratio increases tool lifetime / Na usinagem de roscas internas, ferramentas dedicadas, conhecidas como machos r?gidos s?o necess?rios para cada tipo de perfil e di?metro, al?m de reduzidos valores de velocidade de corte quando comparado aos principais processos de usinagem. Esta restri??o na velocidade de corte est? associada ? dificuldade de sincroniza??o da rota??o e velocidade de avan?o da ferramenta no processo. O fato restringe a flexibilidade e torna os tempos de usinagem longos diante da manufatura de componentes com roscas. Uma alternativa as restri??es impostas pelos machos r?gidos na usinagem de roscas ? o fresamento com a t?cnica de interpola??o helicoidal. A t?cnica ? a fus?o de dois movimentos: rota??o e interpola??o helicoidal. As ferramentas podem ter diferentes configura??es: uma ?nica aresta ou m?ltiplas arestas (no sentido axial, radial ou em ambos). Contudo, o fresamento de roscas com a t?cnica de interpola??o helicoidal ? relativamente novo e restritas pesquisas existem sobre o tema, fato que promove desafios para sua ampla aplica??o no ambiente de manufatura. O objetivo desta pesquisa ? determinar o desempenho dos diferentes tipos de ferramentas no fresamento de roscas com a t?cnica de interpola??o helicoidal em a?os endurecidos. Neste sentido, quatro ferramentas com diferentes configura??es foram utilizadas para usinagem de roscas em a?o AISI 4340 no estado temperado e revenido (40 HRC de dureza). Os resultados mostraram que a utiliza??o do corte concordante possibilitou a usinagem de um maior n?mero de roscas, independentemente do tipo de ferramenta. A utiliza??o do corte discordante causou avaria de lascamento nas arestas de corte, enquanto que o corte concordante promoveu desgaste abrasivo. Outro ponto relevante ? que o aumento da rela??o di?metro do furo e di?metro da ferramenta possibilitou incremento da vida da ferramenta

L'utilisation croissante des polymères dans les structures industrielles est impulsée par le besoin de réduction du cycle/coût de production ainsi que de l'allègement des structures. Dans l'industrie automobile, PSA Peugeot Citroën s'est lancé sur une problématique liée au dimensionnement d'un procédé d'assemblage de pièces plastiques par vissage-taraudage. Le principe du procédé consiste à réaliser le taraudage directement lors du montage de la pièce <<portée>> en polymère en utilisant une vis métallique auto-taraudeuse. Il s'agissait alors d'être capable de modéliser numériquement par éléments finis l'opération de vissage-taraudage. Cet outil numérique offre ensuite la possibilité de mener des plans d'expériences plus larges en étudiant l'influence d'un plus grand nombre de paramètres à des fins d'optimisation de procédé d'assemblage impliquant les polymères. Les premières investigations ont montré qu'il s'agissait d'un problème thermo-mécanique complexe où toutes les composantes de déformation des matériaux polymères sont sollicitées : élastique, visqueuse, plastique et volumique. La démarche suivie est donc celle de l'approche locale de la rupture qui nécessite des observations fines des micro-mécanismes de déformation et d'endommagement suivies d'une modélisation par éléments finis s'inspirant de ces micro-mécanismes. Les données expérimentales se basent sur les variables mesurables à partir des essais mécaniques, enrichies par des observations en tomographie X. Cette technique non destructive révélant des images en 3D a permis de caractériser la morphologie et la distribution de la porosité en fond de filet. La prise en compte de cette porosité a été réalisée à l'aide d'un modèle issu de la mécanique des milieux poreux : le modèle de Gurson-Tvergaard-Needleman adapté aux matériaux polymères. Le modèle identifié a permis de construire un diagramme sur lequel peut s'appuyer le choix de la vitesse de rotation optimale du procédé de vissage-taraudage. Une alternative consistant en un assemblage de type vis polymère/écrou polymère a été également étudiée. Grâce à l'approche locale dont le critère de rupture est basé sur la porosité critique, le point faible de l'assemblage ainsi que sa tenue mécanique présumée à partir du niveau d'endommagement atteint en ce point ont pu être estimés. / The increasing use of polymers in engineering structures is promoted by the need to reduce both cycle/cost production and the weight of these structures. PSA Peugeot Citroën initiated research works to design the assembling process using metallic screwing/threading on polymers. It consists in directly taping the polymeric piece during the mounting operation by using self-threading metallic screw. The final objective of the work deals with the ability to numerically (finite element) model the screwing/threading operation. This numerical tool offers the possibility to perform a large campaign of study highlighting the sensitivity of the assembly procedure to a significant range of parameters. The first investigations showed that this problem consisted of complex thermo-mechanical loading for which all the deformation components of the polymeric material were involved: elastic, viscous, plastic and volumetric. The study was performed within the framework of the local approach to fracture, that required fine examinations of the micro-mechanisms of deformation and damage within the polymer. The experimental database were composed of measurable variables obtained from mechanical tests together with a comprehensive X-ray tomographic inspections. This latter non destructive technique revealing 3D images of the deformed microstructure allowed for characterization of the morphology and the distribution of voids within the polymer in the vicinity of the crest. To account for void volume fraction, a model from the mechanics of porous media was utilized: the Gurson-Tvergaard-Needleman model, modified for polymeric materials studies. The present model allowed for a construction of a failure assessment diagram that would permit to optimize the screwing rotation speed of the screwing-tapping process. An alternative solution consisting of an assembly composed of polymeric screw and polymeric nut was additionally investigated. Thanks to the local approach of fracture criterion based on the critical porosity, the weakest point of the assembly as well as its mechanical residual strength were estimated.

Parallel programming models are quite challenging and emerging topic in the parallel computing era. These models allow a developer to port a sequential application on to a platform with more number of processors so that the problem or application can be solved easily. Adapting the applications in this manner using the Parallel programming models is often influenced by the type of the application, the type of the platform and many others. There are several parallel programming models developed and two main variants of parallel programming models classified are shared and distributed memory based parallel programming models. The recognition of the computing applications that entail immense computing requirements lead to the confrontation of the obstacle regarding the development of the efficient programming models that bridges the gap between the hardware ability to perform the computations and the software ability to support that performance for those applications [25][9]. And so a better programming model is needed that facilitates easy development and on the other hand porting high performance. To answer this challenge this thesis confines and compares four different shared memory based parallel programming models with respect to the development time of the application under a shared memory based parallel programming model to the performance enacted by that application in the same parallel programming model. The programming models are evaluated in this thesis by considering the data parallel applications and to verify their ability to support data parallelism with respect to the development time of those applications. The data parallel applications are borrowed from the Dense Matrix dwarfs and the dwarfs used are Matrix-Matrix multiplication, Jacobi Iteration and Laplace Heat Distribution. The experimental method consists of the selection of three data parallel bench marks and developed under the four shared memory based parallel programming models considered for the evaluation. Also the performance of those applications under each programming model is noted and at last the results are used to analytically compare the parallel programming models. Results for the study show that by sacrificing the development time a better performance is achieved for the chosen data parallel applications developed in Pthreads. On the other hand sacrificing a little performance data parallel applications are extremely easy to develop in task based parallel programming models. The directive models are moderate from both the perspectives and are rated in between the tasking models and threading models. / From this study it is clear that threading model Pthreads model is identified as a dominant programming model by supporting high speedups for two of the three different dwarfs but on the other hand the tasking models are dominant in the development time and reducing the number of errors by supporting high growth in speedup for the applications without any communication and less growth in self-relative speedup for the applications involving communications. The degrade of the performance by the tasking models for the problems based on communications is because task based models are designed and bounded to execute the tasks in parallel without out any interruptions or preemptions during their computations. Introducing the communications violates the purpose and there by resulting in less performance. The directive model OpenMP is moderate in both aspects and stands in between these models. In general the directive models and tasking models offer better speedup than any other models for the task based problems which are based on the divide and conquer strategy. But for the data parallelism the speedup growth however achieved is low (i.e. they are less scalable for data parallel applications) are equally compatible in execution times with threading models. Also the development times are considerably low for data parallel applications this is because of the ease of development supported by those models by introducing less number of functional routines required to parallelize the applications. This thesis is concerned about the comparison of the shared memory based parallel programming models in terms of the speedup. This type of work acts as a hand in guide that the programmers can consider during the development of the applications under the shared memory based parallel programming models. We suggest that this work can be extended in two different ways: one is from the developer‘s perspective and the other is a cross-referential study about the parallel programming models. The former can be done by using a similar study like this by a different programmer and comparing this study with the new study. The latter can be done by including multiple data points in the same programming model or by using a different set of parallel programming models for the study. / C/O K. Manoj Kumar; LGH 555; Lindbloms Vägan 97; 37233; Ronneby. Phone no: 0738743400 Home country phone no: +91 9948671552

III-nitridy běžně krystalizují v hexagonální (wurtzitové) struktuře, zatímco kubická (sfaleritová) struktura je metastabilní a má pouze mírně vyšší energii. Jejich fyzikální vlastnosti jsou silně ovlivněny přítomností rozsáhlých defektů, které jsou v těchto dvou strukturách od sebe odlišné. U wurtzitových nitridů se jedná primárně o vláknové dislokace. Některé vláknové dislokace tvoří hluboké energetické stavy v zakázaném pásu, kterými ovlivňují elektrické a optoelektronické vlastnosti těchto materiálů. Oproti tomu, kubické nitridy obsahují množství vrstevných chyb, které představují lokální transformace do stabilnější wurtzitové struktury. Cílem této práce je charakterizovat rozsáhlé defekty v obou krystalových strukturách pomocí elektronové mikroskopie, mikroskopie atomárních sil a rentgenové difrakce. Prokázali jsme, že vzorky GaN/AlN a AlN s orientací (0001) rostlé na substrátu Si (111) pomocí epitaxe z organokovových sloučenin obsahují velkou hustotu vláknových dislokací. Nejčastější jsou dislokace s Burgersovým vektorem s komponentou ve směru a wurtzitové struktury, následované dislokacemi s Burgersovým vektorem s komponentou ve směru a+c, zatímco dislokace s Burgersovým vektorem s c komponentou jsou relativně vzácné. Pravděpodobný původ vláknových dislokací je diskutován v souvislosti s různými mechanismy růstu těchto vrstev. Prizmatické vrstevné chyby byly nalezeny v tenkých nukleačních vrstvách AlN, ale v tlustších vrstvách již nebyly přítomny. Na rozhraní AlN / Si byla nalezena amorfní vrstva složená ze SiNx a částečně taky z AlN. Navrhujeme, že by tato amorfní vrstva mohla hrát významnou roli při relaxaci misfitového napětí. Analýza elektrické aktivity rozsáhlých defektů v AlN byla provedena pomocí měření proudu indukovaného elektronovým svazkem. Zjistili jsme, že vláknové dislokace způsobují slabý pokles indukovaného proudu. Díky jejich vysoké hustotě a rovnoměrnému rozložení však mají větší vliv na elektrické vlastnosti, než mají V-defekty a jejich shluky. Topografické a krystalografické defekty byly studovány na nežíhaných a žíhaných nukleačních vrstvách kubického GaN deponovaných na 3C-SiC (001) / Si (001) substrátu. Velikost ostrůvků na nežíhaných vzorcích se zvyšuje s tloušťkou nukleační vrstvy a po žíhání se dále zvětšuje. Po žíhání se snižuje pokrytí substrátu u nejtenčích nukleačních vrstev v důsledku difúze a desorpce (nebo leptání atmosférou reaktoru). Vrstevné chyby nalezené ve vrstvách GaN, poblíž rozhraní se SiC, byly většinou identifikovány jako intrinsické a byly ohraničené Shockleyho parciálními dislokacemi. Jejich původ byl diskutován, jako i vliv parciálních dislokací na relaxaci misfitového napětí. Díky velkému množství vrstevných chyb byly podrobněji studovány jejich interakce. Na základě našich zjištění jsme vyvinuli teoretický model popisující anihilaci vrstevných chyb v kubických vrstvách GaN. Tento model dokáže předpovědět pokles hustoty vrstevných chyb se zvyšující se tloušťkou vrstvy.