On board processor system study Final report

Development and characteristics of onboard processor syste

Investigation of charge coupled device correlation techniques

Analog Charge Transfer Devices (CTD's) offer unique advantages to signal processing systems, which often have large development costs, making it desirable to define those devices which can be developed for general system's use. Such devices are best identified and developed early to give system's designers some interchangeable subsystem blocks, not requiring additional individual development for each new signal processing system. The objective of this work is to describe a discrete analog signal processing device with a reasonably broad system use and to implement its design, fabrication, and testing

Design study of a low cost civil aviation GPS receiver system

A low cost Navstar receiver system for civil aviation applications was defined. User objectives and constraints were established. Alternative navigation processing design trades were evaluated. Receiver hardware was synthesized by comparing technology projections with various candidate system designs. A control display unit design was recommended as the result of field test experience with Phase I GPS sets and a review of special human factors for general aviation users. Areas requiring technology development to ensure a low cost Navstar Set in the 1985 timeframe were identified

Hardware / Software System for Portable and Low-Cost Genome Assembly

“The enjoyment of the highest attainable standard of health is one of the fundamental rights of every human being without distinction of race, religion, political belief, economic or social condition” [56]. Genomics (the study of the entire DNA) provides such a standard of health for people with rare diseases and helps control the spread of pandemics. Still, millions of human beings are unable to access genomics due to its cost, and portability. In genomics, DNA sequencers digitise DNA information, and computers analyse the digitised information. We have desktop and thumb-sized DNA sequencers, that digitise the DNA data rapidly. But computations necessary for the analysis of this data are inevitably performed on high-performance computers (HPCs) and cloud computers. These computations not only require powerful computers but also necessitate high-speed networks since the data generated are in the hundreds of gigabytes. Relying on HPCs and high-speed networks, deny the benefits that can be reaped by genomics for the masses who live in remote areas and in poorer nations. Developing a low-cost and portable genomics computation platform would provide personalised treatment based on an individual’s DNA and identify the source of the fast-spreading epidemics in remote areas and areas without HPC or network infrastructure. But developing a low-cost and portable genome analysing computing platform is a challenging task. This thesis develops novel computer architecture solutions to assemble the whole human DNA and COVID-19 virus RNA on a low-cost and portable platform. The first phase of the solution describes a ring-pipelined processor architecture for a key genome assembly algorithm. The human genome is partitioned to fit into the small memory footprint of embedded processors. These techniques allow an entire human genome to be assembled using highly portable and low-cost embedded processor cores. These processor cores can be housed within a single chip. Each processor was only 0.08 mm 2 and consumed just 37.5 mW. It has only 2 GB memory, 32-bit instruction width, and a clock with a 1 GHz frequency. The second phase of the solution describes how application-specific instruction-set processors can be sped up to execute a key genome assembly algorithm. A fully automated design system is presented, which improves the performance of large applications (such as genome assembly algorithm) and generates application-specific instructions for a commercial processor design tool (Xtensa). The tool enhances the base processor, which was used in the ring pipeline processor architecture. Thus, the alignment algorithms execute 2.1 times faster with only 11% additional hardware. The energy-delay product was reduced by 7.3× compared to the base processor. This tool is the only one of its type which can handle applications which are large. The third phase of the solution designs a portable low-cost genome assembly computer (PGA). PGA enhances the ring pipeline architecture with the customised processor found in phase two and with improved inter-processor communication. The results show that the COVID-19 virus RNA can be assembled in under 10 minutes and the whole human genome can be assembled in 11 days on a portable platform (HPC take around two days) for 30× coverage. PGA has an area footprint of just 5.68 mm 2 in a 28 nm technology node and is far smaller than a high-performance computer processor chip. The PGA consumes only 4W of power, which is lower than the power requirement of a high-performance processor chip. The manufacturing cost of the PGA also would be much cheaper than the high-performance system cost, when produced in volume. The developed solution can be powered by a USB port of a laptop. This thesis is the first of its type to show the design of a single-chip solution to be able to process a complex genomic problem. This thesis contributes to attaining one of the fundamental rights of every human being wherever they may live

Latch-based RISC-V core with popcount instruction for CNN acceleration

Energy-efficiency is essential for vast majority of mobile and embedded battery-powered systems. Internet-of-Things paradigm combines requirements for high computational capabilities, extreme energy-efficiency and low-cost. Increasing manufacturing process variations pose formidable challenges for deep-submicron integrated circuit designs. The effects of variation are further exacerbated by lowered voltages in energy-efficient designs. Compared to traditional flip-flop-based design, latch-based design offers area, energy-efficiency and variation tolerance benefits at the cost of increased timing behavior complexity. A method for converting flip-flop-based processor core to latch-based core at register-transfer-level is presented in this work. Convolutional neural networks have enabled image recognition in the field of computer vision at unprecedented accuracy. Performance and memory requirements of canonical convolutional neural networks have been out of reach for low-cost IoT devices. In collaboration with Tampere University, a custom popcount instruction was added to the cores for accelerating IoT optimized vehicle classification convolutional neural network. This work compares simulation results from synthesized flip-flop-based and latch-based versions of a SCR1 RISC-V processor core and the effects of custom instruction for CNN acceleration. The latch core achieved roughly 50\% smaller energy per operation than the flip-flop core and 2.1x speedup was observed in the execution of the CNN when using the custom instruction

Single-Molecule Detection of Unique Genome Signatures: Applications in Molecular Diagnostics and Homeland Security

Single-molecule detection (SMD) offers an attractive approach for identifying the presence of certain markers that can be used for in vitro molecular diagnostics in a near real-time format. The ability to eliminate sample processing steps afforded by the ultra-high sensitivity associated with SMD yields an increased sampling pipeline. When SMD and microfluidics are used in conjunction with nucleic acid-based assays such as the ligase detection reaction coupled with single-pair fluorescent resonance energy transfer (LDR-spFRET), complete molecular profiling and screening of certain cancers, pathogenic bacteria, and other biomarkers becomes possible at remarkable speeds and sensitivities with high specificity. The merging of these technologies and techniques into two different novel instrument formats has been investigated. (1) The use of a charge-coupled device (CCD) in time-delayed integration (TDI) mode as a means for increasing the throughput of any single molecule measurement by simultaneously tracking and detecting single-molecules in multiple microfluidic channels was demonstrated. The CCD/TDI approach allowed increasing the sample throughput by a factor of 8 compared to a single-assay SMD experiment. A sampling throughput of 276 molecules s-1 per channel and 2208 molecules s-1 for an eight channel microfluidic system was achieved. A cyclic olefin copolymer (COC) waveguide was designed and fabricated in a pre-cast poly(dimethylsiloxane) stencil to increase the SNR by controlling the excitation geometry. The waveguide showed an attenuation of 0.67 dB/cm and the launch angle was optimized to increase the depth of penetration of the evanescent wave. (2) A compact SMD (cSMD) instrument was designed and built for the reporting of molecular signatures associated with bacteria. The optical waveguides were poised within the fluidic chip at orientation of 90° with respect to each other for the interrogation of single-molecule events. Molecular beacons (MB) were designed to probe bacteria for the classification of Gram +. MBs were mixed with bacterial cells and pumped though the cSMD which allowed S. aureus to be classified with 2,000 cells in 1 min. Finally, the integration of the LDR-spFRET assay on the cSMD was explored with the future direction of designing a molecular screening approach for stroke diagnostics

Second year technical report on-board processing for future satellite communications systems

Advanced baseband and microwave switching techniques for large domestic communications satellites operating in the 30/20 GHz frequency bands are discussed. The nominal baseband processor throughput is one million packets per second (1.6 Gb/s) from one thousand T1 carrier rate customer premises terminals. A frequency reuse factor of sixteen is assumed by using 16 spot antenna beams with the same 100 MHz bandwidth per beam and a modulation with a one b/s per Hz bandwidth efficiency. Eight of the beams are fixed on major metropolitan areas and eight are scanning beams which periodically cover the remainder of the U.S. under dynamic control. User signals are regenerated (demodulated/remodulated) and message packages are reformatted on board. Frequency division multiple access and time division multiplex are employed on the uplinks and downlinks, respectively, for terminals within the coverage area and dwell interval of a scanning beam. Link establishment and packet routing protocols are defined. Also described is a detailed design of a separate 100 x 100 microwave switch capable of handling nonregenerated signals occupying the remaining 2.4 GHz bandwidth with 60 dB of isolation, at an estimated weight and power consumption of approximately 400 kg and 100 W, respectively

Long walk to genomics : history and current approaches to genome sequencing and assembly

Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing methods to Next-Generation Sequencing platforms. We then focus on the advantages and challenges of the current technologies and approaches, collectively known as Third Generation Sequencing. As these technical advancements have been accompanied by progress in analytical methods, we also review the bioinformatic tools currently employed in de novo genome assembly, as well as some applications of Third Generation Sequencing technologies and high-quality reference genomes