Two-dimensional (2D) layered materials such as MoS2 have been recognized as high on-off ratio semiconductors which are promising candidates for electronic and optoelectronic devices. In addition to the use of individual 2D materials, the accelerated field of 2D heterostructures enables even greater functionalities. Device designs differ, and they are strongly controlled by the electronic band alignment. For example, photovoltaic cells require type II heterostructures for light harvesting, and light-emitting diodes benefit from multiple quantum wells with the type I band alignment for high emission efficiency. The vertical tunneling field-effect transistor for next-generation electronics depends on nearly broken-gap band alignment for boosting its performance. To tailor these 2D layered materials toward possible future applications, the understanding of 2D heterostructure band alignment becomes critically important. In the first part of this thesis, we discuss the band alignment of 2D heterostructures. To do so, we firstly study the interlayer coupling between two dissimilar 2D materials. We conclude that a post-anneal process could enhance the interlayer coupling of as-transferred 2D heterostructures, and heterostructural stacking imposes similar symmetry changes as homostructural stacking. Later, we precisely determine the quasi particle bandgap and band alignment of the MoS2/WSe2 heterostructure by using scan tunneling microscopy/spectroscopy (STM/S) and micron-beam X-ray photoelectron spectroscopy (μ-XPS) techniques. Lastly, we prove that the band alignment of 2D heterojunctions can be accurately predicted by Anderson’s model, which has previously failed to predict conventional bulk heterostructures. In the second part of this thesis, we develop a new Chemical Vapor Deposition (CVD) method capable of precisely controlling the growth area of p- and n-type transition metal dichalcogenides (TMDCs) and further form lateral or vertical 2D heterostructures. This method also allows p- and n-type TMDCs to separately grow in a selective area in one step. In addition, we demonstrate a first bottom-up 2D complementary inverter based on hetero-TMDCs.

This thesis describes ideas and theories behind machine translatinon, informs the reader about existing machine translation system Moses and by utilizing it proposes system, which is able to learn and later translate from Czech language into Slovak language.

Three-dimensional (3D) structure of a protein is essential as the guidance of structure-based drug dis-covery. To achieve robust homology modeling with atomic-level accuracy, reliable loop predictions are required. Here, a novel hierarchical protocol of Protein Local Optimization Program (PLOP) is designed to produce sub-2 angstrom predictions on loop regions in homology modeling. Dramatic improvements in both speed and accuracy have been realized with implementation of special-designed clustering and adaptive loop closure algorithm. Four prediction rounds are designed for homology modeling as the high-level protocol of PLOP, which allows latter rounds employ the educated guess of backbone atom positions and hydrogen bonding information inherited from the previous rounds, contributing to additional prediction accuracy. The success of PLOP has been demonstrated with four different data sets, mainly concen-trating on homology modeling of H3 loops of antibodies. GPU-accelerated sampling algorithm and deep learning models are implemented, which are able to produce promising predictions as input templates for PLOP in the context of homology modeling.

Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts.

INTRODUCTION: Spinal deformities, including adult spinal deformities (ASD) and adolescent idiopathic scoliosis (AIS), can cause significant pain and disability. Radiographic parameters are measured in order to establish quantitative relationships among spinal alignment and health related quality of life metrics. Various classification systems including the Scoliosis Research Society (SRS)-Schwab and Global Alignment Proportion (GAP) score have been developed to correlate radiographic parameters with relevant clinical outcomes. While the SRS-Schwab Classification is both a coronal and sagittal categorization that correlates to health related quality of life metrics, the GAP score is a newly developed 13-point scale that focuses on sagittal alignment to predict mechanical failure postoperatively. The study aims to evaluate the utility of the GAP score as a method of evaluating radiographic correction and maintenance over one year. METHODS: This was a retrospective analysis of ASD and AIS patients who underwent operative intervention. Patients were evaluated for GAP score changes from preoperative to postoperative and then to a one year follow up. Of the 285 screened patients, 73 had suitable radiographs for measurements. This included 45 ASD patients, 32 of which had one year follow up radiographs, and 28 AIS patients, of which only 19 had one year follow up radiographs. Measurements were obtained by three independent readers. These included pelvic incidence (PI), pelvic tilt (PT), L1-S1 lumbar lordosis (L1-S1 LL), L4-S1 lumbar lordosis (L4-S1 LL), sacral slope (SS), global tilt (GT), and sagittal vertical axis (SVA). GAP score subcategories were calculated and summed to produce the GAP score. RESULTS: The 73 included patients had an average age of 41.8 ± 24.1, BMI of 26.2 ±6.3, and consisted of 51 females (69.9%). All but one radiographic parameters exhibited an Intra Class Correlation (ICC) of over 0.66. PI had an ICC of 0.59 which was likely due to the incomplete visibility of the femoral heads in few radiographs. Among ASD patients, from pre to postoperative, PI-LL significantly decreased from 18° to 5°, PT significantly decreased from 26° to 19°, L1-S1 LL significantly increased from 37° to 47°, L4-S1 LL significantly increased from 28° to 31°, GT significantly decreased from 37° to 25°, SVA significantly decreased from 120 mm to 64 mm, and total GAP score significantly decreased from 8 to 6. For the 32 patients with long term data, the GAP score changed significantly from 9 to 6 to 7 at one year follow up. Of the 32 patients, 14 patients experienced a worsened score at the one year follow up. Among AIS patients, PI-LL increased from 0° to 3°, PT remained 13°, L1-S1 LL decreased from 56° to 53°, L4-S1 LL significantly decreased from 37° to 31°, GT increased from 14° to 16°, SVA decreased from 25 mm to 28 mm, and total GAP score increased from 3 to 4. For the 19 with long term data, the GAP score changed significantly from 3 to 3 to 2 and 2 patients experienced a worsened score at the one year follow up. DISCUSSION: The patient population showed a slight improvement in GAP score among both ASD and AIS groups. The improvement is more pronounced when evaluating with the SRS-Schwab Classification. The GAP score does not emphasize the same radiographic parameters and therefore does not correlate well with the SRS-Schwab Classification. Many patients also experienced a worsened GAP score by the one year follow up which can be attributed to the adjacent superior or inferior region (PJK), thoracolumbar region (construct failure), or compensation at the pelvis through hip flexion. Additionally, GAP is potentially oversensitive to measurement error and rounding differences. Thus, the utility of the GAP score in evaluating spinal deformity patients is questionable and requires further adjustment and evaluation based on prospective studies.

Colouration is an important phenotypic trait of animals and plays a substantial role in the characteristics of individual animal species. The MC1R gene has an essential role in colouration. This thesis is focused on the study of sequence variability in this gene and subsequent phylogram formation in selected species, which are: Bos Primigenius Taurus, Sus Scrofa, Equus Caballus and Canis Lupus Familiaris. There were custom primers designed in Oligo for the selected exon sequence. Based on se-quencing, known polymorphisms in Canis Lupus Familiaris and Equus Caballus were detected. In Canis Lupus Familiaris sequence, there was a 790 A>G polymorphism. All of N sequenced samples (N = 10) carried the E (790AA) allele. In Equus Caballus se-quence, there was a 901 C>T polymorphism, with representatives of all genotypes nEE(901CC) = 2, nEe(901CT) = 2, nee(901TT) = 6. The thesis also provides a comprehensive overview of the phylogenetic tree for-mation process. For phylogenetic analysis, there were added sequences from other ani-mal species, gained from freely available genomic databases. The reconstruction took place in the MEGA X program with selected distance and sign methods. Only nodes with bootstrap support ≥ 70 could be interpreted. JC69 and HKY85 models were cho-sen as substitution models. The choice of models was statistically supported by testing likelihood in the Model Generator with P < 0,0001 support. The trees obtained by par-ticular methods were compared by the Pearson correlation coefficient.

Data is distributed across interconnected relations in relational databases. Relationships between tuples can be rearranged in distinct relations by matching the values of the join attribute, a process called equi-join operation. Unlike standard attempts to design efficient join algorithms in this thesis, an approach is proposed to align tuples in relation so that joins can be readily and effectively done. We position tuples in their respective relationships, called relations alignment, which has matching join attribute values in the corresponding positions. We also address how to align relations and perform joins on aligned relations. The experiments were conducted in this research to measure and analyze the efficiency of the proposed approach compared to standard MySQL joins.

In this dissertation, new ways for controlling the internal structures of a system of polymer composites, polymer blends, and hydrogel composites by means of external electric or magnetic fields are presented. The first part of this study addresses the development of an anisotropic phase-separated morphology in polymer blends by using electrically pre-oriented clay particles. It was observed that electrically pre-oriented montmorillonite clay particles in a homogenous single-phase blend lead to anisotropic phase-separated morphology of the blends, undergoing demixing upon temperature shift to a two-phase regime. The initial co-continuous microstructure developed into a coarsened and directionally organized phase-separated morphology parallel to the direction of oriented clay particles (applied AC electric field direction) over the annealing time. It was also found that the degree of clay orientation under AC electric field was linearly proportional to the degree of polymer-phase orientation. The temporal morphological evolution was thoroughly analyzed by electron microscopy and X-ray diffraction studies. The second part of the study covers anisotropic hydrogel nanocomposites developed by orienting magnetically sensitive nontronite clay minerals under the strong magnetic fields. Anisotropic hydrogel nanocomposites were formed by magnetic-field assisted orientation of nontronite clays suspended in a hydrogel precursor solution followed by a gelation process. The degree of orientation of nontronite minerals was quantitively characterized by birefringence and small-angle X-ray scattering. The resultant hydrogels exhibited anisotropic optical, mechanical, and swelling properties along the direction of oriented clay minerals. Anisotropic water swelling behaviors can be particularly applied in medical dressing materials, where vertical wicking of fluid into the wound dressing is sought after for minimizing periwound maceration damage.

Wireless communication systems utilize the wireless medium to perform over-the-air (OTA) data transfer. There are many factors that can impact the quality of wireless communications, such as medium imperfection, interfering environment, mismatch of transceivers, etc. To mitigate these problems and improve the quality of service (QoS), this research study is conducted on three important topics including synchronization techniques, impairment estimation theory and techniques, and interference alignment techniques. In this thesis, it firstly present a dual link algorithm to align and manage the interference of multiple-input and multiple-output (MIMO) networks. A field-programmable gate array (FPGA) prototype is designed for software defined radio (SDR) platforms. As one of the key components, a hardware efficient architecture is proposed for the implementation of singular value decomposition (SVD). Secondly, it proposes a maximum-likelihood (ML) based synchronization approach for carrier frequency synchronization for MIMO systems. The algorithm is also implemented on FPGA for real-time performance evaluation. Finally, as an exemplary study of machine learning techniques for wireless communications, a neural network (NN) based estimator is proposed to perform coarse frequency offset estimations for MIMO systems. The proposed NN based estimator can accommodate various channel models and the results show promising performance in terms of accuracy and estimation range. In summary, this thesis provides a comprehensive study on interference alignment, carrier synchronization, and impairment estimation using different approaches. Efficient hardware implementations for the key algorithms are also presented.

Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of 'tree quality'. In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.