High-throughput next-generation sequencing techniques have hugely decreased the cost and increased the speed of sequencing, resulting in an explosion of sequencing data. This motivates the development of high-efficiency sequence alignment algorithms. In this thesis, I present multiple bit-parallel and Single Instruction Multiple Data (SIMD) algorithms that greatly accelerate the processing of biological sequences. The first chapter describes the BitPAl bit-parallel algorithms for global alignment with general integer scoring, which assigns integer weights for match, mismatch, and insertion/deletion. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations. Bit-parallelism has previously been applied to other pattern matching problems, producing fast algorithms. In timed tests, we show that BitPAl runs 7 - 25 times faster than a standard iterative algorithm. The second part involves two approaches to alignment with substitution scoring, which assigns a potentially different substitution weight to every pair of alphabet characters, better representing the relative rates of different mutations. The first approach extends the existing BitPAl method. The second approach is a new SIMD algorithm that uses partial sums of adjacent score differences. I present a simple partial sum method as well as one that uses parallel scan for additional acceleration. Results demonstrate that these algorithms are significantly faster than existing SIMD dynamic programming algorithms. Finally, I describe two extensions to the partial sums algorithm. The first adds support for affine gap penalty scoring. Affine gap scoring represents the biological likelihood that it is more likely for gaps to be continuous than to be distributed throughout a region by introducing a gap opening penalty and a gap extension penalty. The second extension is an algorithm that uses the partial sums method to calculate the tandem alignment of a pattern against a text sequence using a single pattern copy. Next generation sequencing data provides a wealth of information to researchers. Extracting that information in a timely manner increases the utility and practicality of sequence analysis algorithms. This thesis presents a family of algorithms which provide alignment scores in less time than previous algorithms.

This thesis explores the use of an ASIP for handling O-RAN control data. A model application was constructed, optimized and profiled on a simple RV32-IMC core. The compiled code was analyzed, and the instructions “byte swap”, “pack”, bitwise extract/deposit” and “bit field place” were implemented. Synthesis of the core, and profiling of the model application, was done with and without each added instruction. Byte swap had the largest impact on performance (14% improvement per section, and 100% per section extension), followed by bitwise extract/deposit (10% improvement per section but no impact on section extensions). Pack and bit field place had no impact on performance. All instructions had negligible impact on core size, except for bitwise extract/deposit, which increased size by 16%. Further studies, with respect to both overall architecture and further evaluation of instructions to implement, would be necessary to design an ideal ASIP for the application.

This thesis describes an efficient method for speeding up functional verification of arithmetic circuits namely linear network such as wallace trees, counters using linear algebra techniques. The circuit is represented as a network of half adders, full adders and inverters, and modeled as a system of linear equations. The proof of functional correctness of the design is obtained by computing its algebraic signature using standard linear programming (LP) solver and comparing it with the reference signature provided by the designer. Initial experimental results and comparison with Satisfiability Modulo Theorem (SMT) solvers show that the method is efficient, scalable and applicable to complex arithmetic designs, including large multipliers. It is intended to provide a new front end theory/engine to enhance SMT solvers.

Silicon carbide has many properties that make it a promising and desirable material for diverse applications. One such application for silicon carbide wafers is as a transparent cryogenic probe card. This thesis briefly describes the design of a probe card based on a silicon carbide wafer substrate. It includes a description of electroplating fundamentals and demonstrates the feasibility of electroplating copper onto a wafer for the formation of bond pads between the substrate and external PCB ring. The process for electroplating copper with good adhesion and quality based on metal alloy formation, current control, and materials selection is outlined. Results of this process are also presented. This work also demonstrates the ability to machine silicon carbide using electrical discharge machining, abrasive water jet machining, and diamond bit milling, proving diamond grinding to be the most versatile of the described methods for machining intricate patterns into the wafers.

Selective encryption (SE) methods for images often encrypt the sign bits, i.e., the most significant bits (MSBs) of the codewords corresponding to key syntax elements (in compressed images) or to pixel intensities (for uncompressed images). Our work is motivated by the key observation that the binary code (BC) used for these representations has an impact on the quality of the reconstruction at the eavesdropper (Eve), which can be regarded as a measure of the degree of security of the encryption (the lower the quality, the higher the level of security). Therefore, we address the design of BCs that enhance the security of MSB-based SE by increasing the degradation at Eve’s side when she uses a simple replacement attack (replacing all MSBs either by 0s or by 1s). We first consider the scenario of fixed-length BCs, i.e., where all the codewords have the same length. We formulate the design problem as an optimization problem with the objective of maximizing the distortion at Eve’s without any constraint or with a constraint on the entropy of the MSBs in order to shorten the size of the MSB stream to reduce the computational overhead of encryption. We show that the problem can be cast as a binary integer linear program equivalent to a weighted non-bipartite graph matching problem, for which polynomial-time solution algorithms exist. We empirically assess the performance of the optimized BCs on a Mixed Gaussian source, as well as on Gaussian and Laplacian sources, the latter two being commonly used to model the distribution of transform coefficients and prediction residuals. Our experiments lead to the conclusion that MSB-based SE schemes could benefit from the proposed BC designs. For the case of uncompressed images, we also propose a family of structured BCs for the pixel intensity values. These BCs are constructed such that intensity values that are close have reconstructions that are far apart. As a result, the reconstruction with the replacement attack significantly destroys the smooth areas and blurs the edges, therefore increasing the degree of security. Next, we focus on the construction of variable-length BCs for the non-zero quantized AC coefficients in JPEG compressed images. For this, we first formulate the BC design problem as the problem of maximizing the distortion at Eve’s side with a constraint on the entropy. This problem can also be cast as a weighted non-bipartite graph matching problem and, therefore, can be solved efficiently. Furthermore, by gaining insights from the optimization results, a simpler and faster method for BC design is devised, which consists of only swapping a few codewords in the original code used in JPEG. We assess the practical performance of the proposed BCs for the SE method of JPEG images that encrypts only the MSBs of the non-zero quantized AC coefficients, along with the full encryption of the DC coefficients. Our experimental results show that high visual security can be achieved with only a small sacrifice in compression efficiency. In addition, the proposed BCs can be tuned to achieve various levels of degradation at Eve’s side, a property that is convenient for certain applications. / Thesis / Doctor of Philosophy (PhD)

The current focus on the Internet of Things (IoT) has led to the emergence of many network scenarios with unlimited use cases, including smart homes, smart cities, smart agriculture, and more. Unmanned aerial vehicles (UAVs), also known as drones, have become increasingly popular due to their versatility and ability to collect and transmit data through various sensors and cameras. With real-time data transmission, autonomy, and cost-effectiveness, UAVs have become valuable tools for different applications, including disaster management, agriculture monitoring, and remote area control. Low-power wide-area network (LPWAN) technology plays a crucial role in enabling IoT, and LoRaWAN is one of the specific LPWAN communication technologies that can provide low power consumption and coverage over a wide range. During a catastrophe, wireless communication is critical for analyzing damaged regions, coordinating rescue and relief team actions, saving lives, and reducing economic losses. UAVs can partially replace damaged or overloaded wireless networks as an alternative wireless network provider. This thesis aimed to simulate a LoRa network and investigate the relationship between the UAV coverage radius and elevation angle, as well as the effect of multipath distortion and signal attenuation on UAV and user distance. By calculating signal-to-noise ratio (SNR) and bit error rate (BER) for LoRa in a line-of-sight (LoS) and non-line-of-sight (NLoS) environment, we provided a comprehensive analysis of LoRaWAN performance in real-life environments for long distances. The results indicate that LoRaWAN communication is reliable in various environments, making it a promising technology for emergency and medical communications. / Det nuvarande fokuset på Internet of Things (IoT) har lett till uppkomsten av många nätverksscenarier med obegränsade användningsfall, inklusive smarta hem, smarta städer, smart jordbruk och mer. Obemannade flygfarkoster (UAV), även kända som drönare, har blivit allt populärare på grund av deras mångsidighet och förmåga att samla in och överföra data genom olika sensorer och kameror. Med realtidsdataöverföring, autonomi och kostnadseffektivitet har UAVs blivit värdefulla verktyg för olika applikationer, inklusive katastrofhantering, jordbruksövervakning och fjärrkontroll av områden. Low-power wide-area network (LPWAN)-teknik spelar en avgörande roll för att möjliggöra IoT, och LoRaWAN är en av de specifika LPWAN-kommunikationsteknikerna som kan ge låg strömförbrukning och täckning över ett brett spektrum. Under en katastrof är trådlös kommunikation avgörande för att analysera skadade regioner, koordinera räddnings- och hjälpteams åtgärder, rädda liv och minska ekonomiska förluster. UAV:er kan delvis ersätta skadade eller överbelastade trådlösa nätverk som en alternativ leverantör av trådlöst nätverk. Detta examensarbete syftade till att simulera ett LoRa-nätverk och undersöka sambandet mellan UAV-täckningsradien och höjdvinkeln, såväl som effekten av flervägsdistorsion och signaldämpning på UAV och användaravstånd. Genom att beräkna signal-brusförhållande (SNR) och bitfelsfrekvens (BER) för LoRa i en siktlinje (LoS) och icke-siktlinje (NLoS) miljö, gav vi en omfattande analys av LoRaWAN prestanda i verkliga miljöer för långa avstånd. Resultaten indikerar att LoRaWAN-kommunikation är tillförlitlig i olika miljöer, vilket gör den till en lovande teknik för akut- och medicinsk kommunikation.

No / A proposed method for cancelling or reducing the effect of the transmitted power within the transceiver MIMO unit is investigated and discussed using a feedback signal process between the elements. Several parameters including the level of feedback power mismatch, the transmitted power and the received power are considered in this work to test the performance of the system in term of the bit error rate (BER) versus signal to noise ratio (SNR). A new software programme using MATLAB is implemented to evaluate the proposed method. The results showed that the performances of the system are heavily dependent on the amount of the transmitted power, the received power, and the mismatch in the feedback component.

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