Partial VLSI implementation of the architecture for reusable components (ARC)

This work describes a novel VLSI implementation of the Architecture for Reusable Components (ARC) processor, using Hardware Description Language (HDL). The main goal here is to achieve efficient execution of reusable software through proper hardware support. This involves the hard wired implementation of each instruction designed for the ARC processor. Instructions are broken down into their logical functions, then modeled and simulated through the hierarchical design methods that HDL offers. The structural model of the processor has been developed and simulated. The purpose here has been to begin work on the design and implementation of the ARC processor. The instructions were built using HDL modules, and then simulated using a logic simulator. The effect of internal propagation delays in the execution of the logic modules have been investigated. Changes in delay parameters have been applied to obtain correct logic transfer operations. The redundancy in the logic transfer operations have also been investigated to see parallelism at the instruction execution level

Seguimiento 4D de microorganismos con microscopía holográfica digital sin lentes a velocidad de video por medio de GPGPU

Resumen: La presente tesis de Maestría en Ingeniería de Sistemas se centra en el seguimiento 4D de microorganismos a velocidad de video. Por medio de la microscopía holográfica digital sin lentes se adquiere la información del sistema microscópico y con técnicas de reconocimiento de patrones en el procesamiento digital de imágenes se lleva a cabo su seguimiento 4D (espacio 3D y tiempo). Ambas técnicas son implementadas con soporte en la arquitectura GPGPU para su operación a velocidad de video. La validez científica y tecnológica de la tesis subyace en el hecho que el seguimiento de microorganismos a ratas de video potencializará distintas aplicaciones en áreas como la salud, el monitoreo del medio ambiente y el combate del terrorismo biológico, entre otros. La metodología desarrollada en esta tesis permite seguir en 4D microorganismos de dimensiones en el orden de los 100 μm en volúmenes de muestra de 1mm3, a una velocidad máxima de 8 cuadros por segundo.Abstract: This Master’s thesis in Systems Engineering focuses on the monitoring of microorganisms in 4D at video rate. By using digital lensless holographic microscopy the microscopic information of the system is acquired and with pattern recognition techniques in digital image processing it is carried out the tracking in 4D (3D in space and time). Both techniques are implemented in the GPGPU architecture for operation at video rate. The technological and scientific validity of the thesis lies on the fact that the monitoring of microorganisms at video rate will potentiate different applications in areas such as health, environmental monitoring and combating bioterrorism, among others. The methodology developed in this thesis can track in 4D microorganisms of dimensions in the order of 100 μm, in 1 mm3 sample volumes, at a maximum rate of 8 frames per second.Maestrí

An Enhanced Hardware Description Language Implementation for Improved Design-Space Exploration in High-Energy Physics Hardware Design

Detectors in High-Energy Physics (HEP) have increased tremendously in accuracy, speed and integration. Consequently HEP experiments are confronted with an immense amount of data to be read out, processed and stored. Originally low-level processing has been accomplished in hardware, while more elaborate algorithms have been executed on large computing farms. Field-Programmable Gate Arrays (FPGAs) meet HEP's need for ever higher real-time processing performance by providing programmable yet fast digital logic resources. With the fast move from HEP Digital Signal Processing (DSPing) applications into the domain of FPGAs, related design tools are crucial to realise the potential performance gains. This work reviews Hardware Description Languages (HDLs) in respect to the special needs present in the HEP digital hardware design process. It is especially concerned with the question, how features outside the scope of mainstream digital hardware design can be implemented efficiently into HDLs. It will argue that functional languages are especially suitable for implementation of domain-specific languages, including HDLs. Casestudies examining the implementation complexity of HEP-specific language extensions to the functional HDCaml HDL will prove the viability of the suggested approach

A Software Toolchain for Physical System Description and Synthesis, and Applications to Microfluidic Design Automation

Microfluidic circuits are currently designed by hand, using a combination of the designer’s domain knowledge and educated intuition to determine unknown design parameters. As no microfluidic circuit design software exists to assist designers, circuits are typically tested by physically constructing them in silico and performing another design iteration should the prototype fail to operate correctly. Similar to how electronic design automation tools revolutionized the digital circuit design process, so too do microfluidic design packages have the potential to increase productivity for microfluidic circuit designers and allow more complex devices to be designed. Two of the primary software engineering problems to be solved in this space relate to design entry and design synthesis. First, the circuit designer requires a programming language to describe the behaviour and properties of the device they wish to build, and a compiler toolchain to convert this description into a model that can then be processed by other software tools. Second, once such a model is constructed, the remaining portions of the design toolchain must be constructed. It is necessary to implement software that can find unknown design parameters automatically to relieve the designer of much of the complexity that goes into creating such a circuit. Furthermore, automated testing and verification tools must be used to simulate the device and check for correctness and safety requirements before the engineer can have confidence in their design. In this thesis I outline work that has been done towards both of these goals. First, I describe a new programming language that has been developed for the purpose of describing and modelling physical systems, including but not limited to microfluidic circuits. This programming language, called “Manifold”, has been implemented following principles and features of modern functional programming languages, as well as drawing inspiration from VHDL and Verilog, the two industry-standard programming languages for EDA. The Manifold high-level language compiler carries out the process of translating a system description into a domain-agnostic intermediate representation. This representation is then passed to a domain-specific backend compiler which can perform further operations on the design, such as creating simulations, performing verification, and generating appropriate output products. Second, I perform a case study with respect to the creation of such a domain-specific backend for the domain of multi-phase microfluidic circuits. The process involved in taking a circuit description from design entry to device specification has a number of significant steps. I discuss in detail these steps with respect to the design of a multi-way droplet generator circuit. Such a circuit is difficult to design because of the behaviour of the key design parameter, the volume of generated droplets. The design goal is for each droplet generator on the device to produce droplets of a certain specified volume. However, the equation relating the properties of a droplet generator to the predicted droplet volume is complex and contains several nonlinearities, making it very difficult to solve by traditional methods. Recent advances in constraint solvers which can reason about nonlinear equations over real-valued terms make it possible to solve this equation efficiently for a given set of design constraints and goals, and produce many feasible specifications for droplet generators that meet the requirements. Another difficulty in designing these circuits is due to interactions between droplet generators. As the produced droplets have a significant hydrodynamic resistance, they affect the behaviour of the circuit by causing perturbations in the flow rates into the droplet generators. This has the potential to alter the volume of droplets that are being produced. Therefore, a means of regulating or controlling the flow rates must be found. I describe a potential solution in the form of a passive element analogous to a capacitor in an electrical circuit. Once an appropriate value for the capacitor is chosen, it remains to verify that it operates correctly under manufacturing variances in fabrication of the device. To perform this verification, a bounded model checker for real-valued differential equations is employed to demonstrate correctness or discover robustness issues. Furthermore, a simulation file for the MapleSim numerical simulation engine is generated in order to perform whole-design tests for further validation. The sequence in which these steps are performed closely follows the concept of “abstraction refinement” in formal methods, in which successively more detailed models are checked and a failure in one step can invoke a previous step with new information, allowing errors to be caught early and introducing the ability to iterate on the design. I describe such a refinement loop in place in the microfluidics backend that integrates these three steps in a coherent design flow, able to synthesize and verify many specifications for a microfluidic circuit, thereby automating a significant portion of the design process. The combination of the Manifold high-level language and microfluidics backend introduces a new design automation toolchain that demonstrates the effectiveness of constraint solvers in the tasks of design synthesis and verification. Further enhancements to the performance and capabilities of these solvers, as well as to the high-level language and backend, will in the future produce a general-purpose design package for microfluidic circuits that will allow for new, complex designs to be created and checked with confidence

The Genetic Contributions to HAART-Associated Dyslipidemia

Highly active anti-retroviral therapy (HAART) has been successful in delaying the progression to AIDS in HIV infected individuals. Exposure to HAART can result in metabolic side effects such as dyslipidemia and lipodystrophy in a subset of treated patients. We used a custom designed Illumina GoldenGate Genotyping assay to investigate the genetic susceptibility to dyslipidemia attributed to HIV infection and HAART treatment. 1,945 men were selected from the Multicenter AIDS Cohort Study (MACS) for genotyping and phenotypic analysis of serum lipid levels. This population was stratified by biogeographical ancestry and HIV/HAART status. Among men of European ancestry, those who were infected with HIV and receiving HAART had significantly lower serum low-density lipoprotein cholesterol (LDL-C, P = 1.90 x10-4) and high-density lipoprotein cholesterol levels (HDL-C, P < 1.00 x10-7), with significantly higher serum triglyceride (TRIG, P < 1.00 x10-7) levels compared to HIV/HAART (-/-) controls. Among men of mixed African and European ancestry, those who were HIV/HAART (+/+) had significantly lower LDL-C (P = 1.80 x10-4) levels compared to HIV/HAART (-/-) controls. Four SNPs; rs1532624 (P = 1.66 x10-5), rs1532625 (P = 2.36 x10-5), rs711752 (P = 4.48 x10-5), and rs708272 (P = 4.59 x10-5), located in the CETP gene region on chromosome 16 had statistically significant associations with serum HDL-C levels in HIV/HAART (+/+) European men. One SNP, rs261334 (P = 6.53 x10-6), located in the LIPC gene region on chromosome 15 was associated with serum LDL-C levels and another SNP, rs4783961 (P = 9.83 x10-6) located in the CETP gene region, was associated with HDL-C levels in HIV/HAART (+/+) men of mixed African and European ancestry. These results show that dyslipidemia attributed to HAART varies depending on biogeographical ancestry and implicates two genes associated with serum lipid levels in these patients. Understanding the mechanism of HAART-associated dyslipidemia is important to global public health because nearly half of the estimated 30 million individuals infected with HIV are receiving or eligible to receive these drugs and are at risk of these HAART related side effects. Our results can also aid in identifying those individuals at greatest risk of developing HAART-associated dyslipidemia, which could improve monitoring and management of care given to these patients

Integrated Sensing and Communication for Network-Assisted Full-Duplex Cell-Free Distributed Massive MIMO Systems

In this paper, we combine the network-assisted full-duplex (NAFD) technology and distributed radar sensing to implement integrated sensing and communication (ISAC). The ISAC system features both uplink and downlink remote radio units (RRUs) equipped with communication and sensing capabilities. We evaluate the communication and sensing performance of the system using the sum communication rates and the Cramer-Rao lower bound (CRLB), respectively. We compare the performance of the proposed scheme with other ISAC schemes, the result shows that the proposed scheme can provide more stable sensing and better communication performance. Furthermore, we propose two power allocation algorithms to optimize the communication and sensing performance jointly. One algorithm is based on the deep Q-network (DQN) and the other one is based on the non-dominated sorting genetic algorithm II (NSGA-II). The proposed algorithms provide more feasible solutions and achieve better system performance than the equal power allocation algorithm.Comment: 14 pages, 7 figures,submit to China Communication February 28, 2023, date of major revision July 09, 202

A multifunctional setup to record FTIR and UV-vis spectra of organic molecules and their photoproducts in astronomical ices

Laboratory astrophysics and astrochemistr