As techniques for manufacturing and metrology advance, optical systems are being designed with more complexity than ever before. Given these prescriptions, alignment and calibration can be a limiting factor in their final performance. Computer generated holograms (CGHs) have several unique properties that make them powerful tools for meeting these demanding tolerances. This work will present three novel methods for alignment and calibration of optical systems using computer generated holograms. Alignment methods using CGHs require that the optical wavefront created by the CGH be related to a mechanical datum to locate it space. An overview of existing methods is provided as background, then two new alignment methods are discussed in detail. In the first method, the CGH contact Ball Alignment Tool (CBAT) is used to align a ball or sphere mounted retroreflector (SMR) to a Fresnel zone plate pattern with micron level accuracy. The ball is bonded directly onto the CGH substrate and provides permanent, accurate registration between the optical wavefront and a mechanical reference to locate the CGH in space. A prototype CBAT was built and used to align and bond an SMR to a CGH. In the second method, CGH references are used to align axi-symmetric optics in four degrees of freedom with low uncertainty and real time feedback. The CGHs create simultaneous 3D optical references where the zero order reflection sets tilt and the first diffracted order sets centration. The flexibility of the CGH design can be used to accommodate a wide variety of optical systems and maximize sensitivity to misalignments. A 2-CGH prototype system was aligned multiplied times and the alignment uncertainty was quantified and compared to an error model. Finally, an enhanced calibration method is presented. It uses multiple perturbed measurements of a master sphere to improve the calibration of CGH-based Fizeau interferometers ultimately measuring aspheric test surfaces. The improvement in the calibration is a function of the interferometer error and the aspheric departure of the desired test surface. This calibration is most effective at reducing coma and trefoil from figure error or misalignments of the interferometer components. The enhanced calibration can reduce overall measurement uncertainty or allow the budgeted error contribution from another source to be increased. A single set of sphere measurements can be used to calculate calibration maps for closely related aspheres, including segmented primary mirrors for telescopes. A parametric model is developed and compared to the simulated calibration of a case study interferometer.

A central focus of computational biology is to organize and make use of vast stores of molecular sequence data. Two of the most studied and fundamental problems in the field are sequence alignment and phylogeny inference. The problem of multiple sequence alignment is to take a set of DNA, RNA, or protein sequences and identify related segments of these sequences. Perhaps the most common use of alignments of multiple sequences is as input for methods designed to infer a phylogeny, or tree describing the evolutionary history of the sequences. The two problems are circularly related: standard phylogeny inference methods take a multiple sequence alignment as input, while computation of a rudimentary phylogeny is a step in the standard multiple sequence alignment method.Efficient computation of high-quality alignments, and of high-quality phylogenies based on those alignments, are both open problems in the field of computational biology. The first part of the dissertation gives details of my efforts to identify a best-of-breed method for each stage of the standard form-and-polish heuristic for aligning multiple sequences; the result of these efforts is a tool, called Opal, that achieves state-of-the-art 84.7% accuracy on the BAliBASE alignment benchmark. The second part of the dissertation describes a new algorithm that dramatically increases the speed and scalability of a common method for phylogeny inference called neighbor-joining; this algorithm is implemented in a new tool, called NINJA, which is more than an order of magnitude faster than a very fast implementation of the canonical algorithm, for example building a tree on 218,000 sequences in under 6 days using a single processor computer.

No description available.

The Semantic Web is an endeavour to enhance the web with the ability to represent knowledge. The knowledge is expressed through what are called ontologies. In order to make ontologies useful, it is important to be able to match the knowledge represented in different ontologies. This task is commonly known as ontology alignment. Ontology alignment has been studied, but it remains an open problem with an annual competition dedicated to measure alignment tools' performance. Many alignment tools are computationally heavy, require training, or are useful in a specific field of study. We propose an ontology alignment method, NeCO, that builds on clone detection techniques to align ontologies. NeCO inherits the clone detection features, and it is light-weight, does not require training, and is useful for any ontology. / Thesis (Master, Computing) -- Queen's University, 2014-01-29 14:38:52.873

This thesis deals with sequence alignment algorithms. The sequence alignment is a mutual arrange of two or more sequences in order to study their similarity and dissimilarity. Four decades after the seminal work by Needleman and Wunsch in 1970, these methods still need more explorations. We start out with a review of a sequence alignment, and its generalization to multiple alignments, although the focus of this thesis is on the evaluation of the new alignment algorithms. The research presented here in has stepped into the different algorithms that are in terms of the dynamic programming. In the study of sequence alignment algorithms, two powerful techniques have been invented. According to the simulations, the new algorithms are shown to be extremely efficient for the comparing DNA sequences. All the sequence alignment algorithmsare compared in terms of the distance. We use the programming language R for the implementation and simulation of the algorithms discussed in this thesis.

Session ID: FR-G2-2 / Joint 4th International Conference on Soft Computing and Intelligent Systems and 9th International Symposium on advanced Intelligent Systems, September 17-21, 2008, Nagoya University, Nagoya, Japan

The integration of hydrogenated amorphous silicon (a-Si:H) thin-film transistors (TFTs) with plastic substrates enables emerging technologies such as flexible organic light emitting diode (OLED) displays. Current a-Si fabrication processes, however, create residual thin film stress that affects the underlying flexible substrate due to its high mismatch in the coefficient of thermal expansion resulting in a dimensional instability for fabricating TFTs on large area flexible substrates. The motivation of this thesis is to reduce this non-uniformity and improve fabrication throughput of bottom-gated inverted-staggered a-Si:H TFTs on flexible substrates. This thesis therefore encompasses the study of overlay misalignment on TFTs over 3 inch flexible substrates and investigates the electrical characteristics of the TFTs fabricated on plastic platforms. To reduce overlay misalignment of TFTs fabricated on flexible substrates, a plastic-on-carrier lamination process has been developed. The technique comprises of a polyimide tape to attach a 125 um-thick poly-ethylene-napthalate (PEN) flexible substrate to a rigid carrier. This process has been used to minimize stress induced strain of the PEN substrate during the fabrication process; strain, which has been observed after processing a-Si:H TFTs on free-standing substrates. This technique would in turn assist in fabricating uniform stacked-layers as required for a-Si:H TFT fabrication on the PEN substrates. Overlay misalignment is measured after each of the 5 consecutive lithographic steps at 4 corner-most edges of the PEN substrates using a standard optical microscope. Results have shown an overlay misalignment reduction from 21 um to 2 um on average based on the TFTs fabricated on free-standing flexible substrates while ensuring a centre alignment accuracy of +/- 0.5 um. Post fabrication adhesive removal to separate the PEN substrate from the rigid carrier has been accomplished by sample immersion in acetone. The results present a significant increase in fabrication throughput by reducing lithographic overlay misalignment such that the resolution of large-area flexible electronics would be enhanced. Electrical characteristics show the average performance of a-Si:H TFTs with an ON/OFF current ratio of 10^8, field effect mobility of ~0.8 cm^2/Vs, and gate leakage current of 10^-13 A.

To assess the similarities and the differences among protein structures, a variety of structure alignment algorithms and programs have been designed and implemented. We introduce a low-resolution approach and a high-resolution approach to evaluate the similarities among protein structures. Our results show that both the low-resolution approach and the high-resolution approach outperform state-of-the-art methods. For the low-resolution approach, we eliminate false positives through the comparison of both local similarity and remote similarity with little compromise in speed. Two kinds of contact libraries (ContactLib) are introduced to fingerprint protein structures effectively and efficiently. Each contact group from the contact library consists of one local or two remote fragments and is represented by a concise vector. These vectors are then indexed and used to calculate a new combined hit-rate score to identify similar protein structures effectively and efficiently. We tested our ContactLibs on the high-quality protein structure subset of SCOP30, which contains 3,297 protein structures. For each protein structure of the subset, we retrieved its neighbor protein structures from the rest of the subset. The best area under the ROC curve, archived by a ContactLib, is as high as 0.960. This is a significant improvement over 0.747, the best result achieved by the state-of-the-art method, FragBag. For the high-resolution approach, our PROtein STructure Alignment method (PROSTA) relies on and verifies the fact that the optimal protein structure alignment always contains a small subset of aligned residue pairs, called a seed, such that the rotation and translation (ROTRAN), which minimizes the RMSD of the seed, yields both the optimal ROTRAN and the optimal alignment score. Thus, ROTRANs minimizing the RMSDs of small subsets of residues are sampled, and global alignments are calculated directly from the sampled ROTRANs. Moreover, our method incorporates remote information and filters similar ROTRANs (or alignments) by clustering, rather than by an exhaustive method, to overcome the computational inefficiency. Our high-resolution protein structure alignment method, when applied to optimizing the TM-score and the GDT-TS score, produces a significantly better result than state-of-the-art protein structure alignment methods. Specifically, if the highest TM-score found by TM-align is lower than 0.6 and the highest TM-score found by one of the tested methods is higher than 0.5, our alignment method tends to discover better protein structure alignments with (up to 0.21) higher TM-scores. In such cases, TM-align fails to find TM-scores higher than 0.5 with a probability of 42%; however, our alignment method fails the same task with a probability of only 2%. In addition, existing protein structure alignment scoring functions focus on atom coordinate similarity alone and simply ignore other important similarities, such as sequence similarity. Our scoring function has the capacity for incorporating multiple similarities into the scoring function. Our result shows that sequence similarity aids in finding high quality protein structure alignments that are more consistent with HOMSTRAD alignments, which are protein structure alignments examined by human experts. When atom coordinate similarity itself fails to find alignments with any consistency to HOMSTRAD alignments, our scoring function remains capable of finding alignments highly similar to, or even identical to, HOMSTRAD alignments.

The legal reform process in South Africa has led to increasingly complex legislative requirements for new developments in the form of various authorization processes. Currently different organs of state, at different spheres of government exercise a range of powers and functions in respect of the approval of development applications. These authorisations typically relate to planning, water management, heritage resources, environmental management, air quality, etc. In order to improve the efficiency and alignment of authorisation processes there is a serious need to gain a better understanding of the interaction between the different authorisation processes as well as the challenges experienced. This research presents the results of a critical analysis of planning and environmental impact assessment (EIA) authorisation processes in the Mpumalanga Province and examines how authorisation processes are implemented and aligned, how efficient the processes are, why process inefficiencies occur and how the efficiency of processes can be improved. The outcome of the research suggests that there are three main success factors for efficiency, namely the legislative framework that provides for administrative and environmental justice, co-operative governance that provides the basis for good communication, and information and competence that injects expertise into the authorisation process. The so-called 'efficiency triangle' is conceptualised, which clearly illustrates the interaction between these success factors. / Thesis (M. Environmental Management)--North-West University, Potchefstroom Campus, 2010.

The legal reform process in South Africa has led to increasingly complex legislative requirements for new developments in the form of various authorization processes. Currently different organs of state, at different spheres of government exercise a range of powers and functions in respect of the approval of development applications. These authorisations typically relate to planning, water management, heritage resources, environmental management, air quality, etc. In order to improve the efficiency and alignment of authorisation processes there is a serious need to gain a better understanding of the interaction between the different authorisation processes as well as the challenges experienced. This research presents the results of a critical analysis of planning and environmental impact assessment (EIA) authorisation processes in the Mpumalanga Province and examines how authorisation processes are implemented and aligned, how efficient the processes are, why process inefficiencies occur and how the efficiency of processes can be improved. The outcome of the research suggests that there are three main success factors for efficiency, namely the legislative framework that provides for administrative and environmental justice, co-operative governance that provides the basis for good communication, and information and competence that injects expertise into the authorisation process. The so-called 'efficiency triangle' is conceptualised, which clearly illustrates the interaction between these success factors. / Thesis (M. Environmental Management)--North-West University, Potchefstroom Campus, 2010.