A parametric study of a monolithic microfluidic system for on-chip biomolecular separation

A microfabricated poly(dimethylsiloxane) (PDMS) chip containing channel filled with polymer monolith has been developed for on-chip biomolecule separation. Methacrylate monolithic polymers were prepared by photo-initiated polymerization within the channel to serve as a continuous stationary phase. The monolithic polymer was functionalized with a weak anion-exchange ligand, and key parameters affecting the binding characteristics of the system were investigated. The total binding capacity was unaffected by the flow rate of the mobile phase but varied significantly with changes in ionic strength and pH of the binding buffer. The binding capacity decreased with increasing buffer ionic strength, and this is due to the limited available binding sites for protein adsorption resulting from cationic shielding effect. Similarly, the binding capacity decreased with decreasing buffer pH towards the isoelectric point of the protein. A protein mixture, BSA and ovalbumin, was used to illustrate the capacity of the methacrylate-based microfluidic chip for rapid biomolecule separation.

Chip formation mechanism and machinability of wrought duplex stainless steel alloys

This paper investigates the chip formation mechanism and machinability of two-phase materials, such as, wrought duplex stainless steel alloys SAF 2205 and SAF 2507. SEM and optical microscopic details of the frozen cutting zone and chips revealed that the harder austenite phase dissipates in the advancement of the cutting tool, being effectively squeezed out of the softer ferrite phase. Microhardness profiles reveal correlation in hardness from the workpiece material transitioning to the chip. The tool wear (TiAIN + TiN coated solid carbide twist drill) and machining forces were investigated. Tool wear, was dominantly due to the adhesion process which developed from built-up edge formation, is highly detrimental to the flank face. Flute damage was also observed as a major issue in the drilling of duplex alloys leading to premature tool failure. Duplex 2507 shows higher sensitivity to cutting speed during machining and strain hardening at higher velocity and less machinability due to presence of higher percentage of Ni, Mo and Cr.

Quick chip assay using locked nucleic acid modified epithelial cell adhesion molecule and nucleolin aptamers for the capture of circulating tumor cells

The role of circulating tumor cells (CTCs) in disease diagnosis, prognosis, monitoring of the therapeutic efficacy, and clinical decision making is immense and has attracted tremendous focus in the last decade. We designed and fabricated simple, flat channel microfluidic devices polydimethylsiloxane (PDMS based) functionalized with locked nucleic acid (LNA) modified aptamers (targeting epithelial cell adhesion molecule (EpCAM) and nucleolin expression) for quick and efficient capture of CTCs and cancer cells. With optimized flow rates (10 μl/min), it was revealed that the aptamer modified devices offered reusability for up to six times while retaining optimal capture efficiency (>90%) and specificity. High capture sensitivity (92%) and specificity (100%) was observed in whole blood samples spiked with Caco-2 cells (10-100 cells/ml). Analysis of blood samples obtained from 25 head and neck cancer patients on the EpCAM LNA aptamer functionalized chip revealed that an average count of 5 ± 3 CTCs/ml of blood were captured from 22/25 samples (88%). EpCAM intracellular domain (EpICD) immunohistochemistry on 9 oral squamous cell carcinomas showed the EpICD positivity in the tumor cells, confirming the EpCAM expression in CTCs from head and neck cancers. These microfluidic devices also maintained viability for in vitro culture and characterization. Use of LNA modified aptamers provided added benefits in terms of cost effectiveness due to increased reusability and sustainability of the devices. Our results present a robust, quick, and efficient CTC capture platform with the use of simple PDMS based devices that are easy to fabricate at low cost and have an immense potential in cancer diagnosis, prognosis, and therapeutic planning.

Lab-on-a-chip or chip-in-a-lab: challenges of commercialization lost in translation

Lab-on-a-chip technology has been long envisaged to have tremendous commercial potential, owing to the ability of such devices to encapsulate a full range of laboratory processes in a single instrument and operate in a portable manner, rapidly and at low cost. Devices are believed to have potential in fields ranging across medical diagnostics, environmental sampling and a range of consumer products, however, to date very few devices have attained commercial success. This review examines the challenges relating to the commercialization of lab-on-a-chip technology from fundamental research to mass manufacturing and aims to provide insight to both academics and product development specialists the perceived hindrances to commercialization and a strategy by which future work could be translated into commercial success.

Redes-em-Chip : arquiteturas e modelos para avaliação de área e desempenho

Com o advento dos processos submicrônicos, a capacidade de integração de transistores tem atingido níveis que possibilitam a construção de um sistema completo em uma única pastilha de silício. Esses sistemas, denominados sistemas integrados, baseiam-se no reuso de blocos previamente projetados e verificados, os quais são chamados de núcleos ou blocos de propriedade intelectual. Os sistemas integrados atuais incluem algumas poucas dezenas de núcleos, os quais são interconectados por meio de arquiteturas de comunicação baseadas em estruturas dedicadas de canais ponto-a-ponto ou em estruturas reutilizáveis constituídas por canais multiponto, denominadas barramentos. Os futuros sistemas integrados irão incluir de dezenas a centenas de núcleos em um mesmo chip com até alguns bilhões de transistores, sendo que, para atender às pressões do mercado e amortizar os custos de projeto entre vários sistemas, é importante que todos os seus componentes sejam reutilizáveis, incluindo a arquitetura de comunicação. Das arquiteturas utilizadas atualmente, o barramento é a única que oferece reusabilidade. Porém, o seu desempenho em comunicação e o seu consumo de energia degradam com o crescimento do sistema. Para atender aos requisitos dos futuros sistemas integrados, uma nova alternativa de arquitetura de comunicação tem sido proposta na comunidade acadêmica. Essa arquitetura, denominada rede-em-chip, baseia-se nos conceitos utilizados nas redes de interconexão para computadores paralelos. Esta tese se situa nesse contexto e apresenta uma arquitetura de rede-em-chip e um conjunto de modelos para a avaliação de área e desempenho de arquiteturas de comunicação para sistemas integrados. A arquitetura apresentada é denominada SoCIN (System-on-Chip Interconnection Network) e apresenta como diferencial o fato de poder ser dimensionada de modo a atender a requisitos de custo e desempenho da aplicação alvo. Os modelos desenvolvidos permitem a estimativa em alto nível da área em silício e do desempenho de arquiteturas de comunicação do tipo barramento e rede-em-chip. São apresentados resultados que demonstram a efetividade das redes-em-chip e indicam as condições que definem a aplicabilidade das mesmas.

Reuse-based test planning for core-based systems-on-chip

Electronic applications are currently developed under the reuse-based paradigm. This design methodology presents several advantages for the reduction of the design complexity, but brings new challenges for the test of the final circuit. The access to embedded cores, the integration of several test methods, and the optimization of the several cost factors are just a few of the several problems that need to be tackled during test planning. Within this context, this thesis proposes two test planning approaches that aim at reducing the test costs of a core-based system by means of hardware reuse and integration of the test planning into the design flow. The first approach considers systems whose cores are connected directly or through a functional bus. The test planning method consists of a comprehensive model that includes the definition of a multi-mode access mechanism inside the chip and a search algorithm for the exploration of the design space. The access mechanism model considers the reuse of functional connections as well as partial test buses, cores transparency, and other bypass modes. The test schedule is defined in conjunction with the access mechanism so that good trade-offs among the costs of pins, area, and test time can be sought. Furthermore, system power constraints are also considered. This expansion of concerns makes it possible an efficient, yet fine-grained search, in the huge design space of a reuse-based environment. Experimental results clearly show the variety of trade-offs that can be explored using the proposed model, and its effectiveness on optimizing the system test plan. Networks-on-chip are likely to become the main communication platform of systemson- chip. Thus, the second approach presented in this work proposes the reuse of the on-chip network for the test of the cores embedded into the systems that use this communication platform. A power-aware test scheduling algorithm aiming at exploiting the network characteristics to minimize the system test time is presented. The reuse strategy is evaluated considering a number of system configurations, such as different positions of the cores in the network, power consumption constraints and number of interfaces with the tester. Experimental results show that the parallelization capability of the network can be exploited to reduce the system test time, whereas area and pin overhead are strongly minimized. In this manuscript, the main problems of the test of core-based systems are firstly identified and the current solutions are discussed. The problems being tackled by this thesis are then listed and the test planning approaches are detailed. Both test planning techniques are validated for the recently released ITC’02 SoC Test Benchmarks, and further compared to other test planning methods of the literature. This comparison confirms the efficiency of the proposed methods.

A Modular and digitally programmable interface based on band-pass sigma-delta modulator for mixed-signal systems-on-chip

The focus of this thesis is to discuss the development and modeling of an interface architecture to be employed for interfacing analog signals in mixed-signal SOC. We claim that the approach that is going to be presented is able to achieve wide frequency range, and covers a large range of applications with constant performance, allied to digital configuration compatibility. Our primary assumptions are to use a fixed analog block and to promote application configurability in the digital domain, which leads to a mixed-signal interface. The use of a fixed analog block avoids the performance loss common to configurable analog blocks. The usage of configurability on the digital domain makes possible the use of all existing tools for high level design, simulation and synthesis to implement the target application, with very good performance prediction. The proposed approach utilizes the concept of frequency translation (mixing) of the input signal followed by its conversion to the ΣΔ domain, which makes possible the use of a fairly constant analog block, and also, a uniform treatment of input signal from DC to high frequencies. The programmability is performed in the ΣΔ digital domain where performance can be closely achieved according to application specification. The interface performance theoretical and simulation model are developed for design space exploration and for physical design support. Two prototypes are built and characterized to validate the proposed model and to implement some application examples. The usage of this interface as a multi-band parametric ADC and as a two channels analog multiplier and adder are shown. The multi-channel analog interface architecture is also presented. The characterization measurements support the main advantages of the approach proposed.

Redes-em-chip de baixo custo

Com as recentes tecnologias de fabricação é possível integrar milhões de transistores em um único chip, permitindo a criação dos chamados System-on-Chip (SoCs), que integram em um único chip um grande número de componentes (tipicamente blocos reutilizáveis conhecidos por núcleos). Quanto mais complexos forem estes sistemas, melhores técnicas de projeto serão necessárias para também reduzir o tempo e custo do projeto. Uma destas técnicas, chamada de Network-on-Chip (NoC), permite melhorar a performance da comunicação entre os núcleos e, ao mesmo tempo, fornecer uma plataforma de comunicação escalável e que pode ser reutilizada para um grande número de sistemas. Uma NoC pode ser definida como uma estrutura de roteadores e canais ponto-a-ponto que interconectam os núcleos de um sistema, provendo o suporte de comunicação entre eles. Os dados são transmitidos pela rede na forma de mensagens, que podem ser divididas em unidades menores chamadas de pacote. Uma das desvantagens desta plataforma de comunicação é o impacto na área do sistema causado pelos roteadores. Dentro deste contexto, este trabalho apresenta uma arquitetura de roteador de baixo custo, com o objetivo de permitir o uso de NoCs em sistemas onde a área do roteador representará um grande impacto no custo do sistema. A arquitetura deste roteador, chamado de Tonga, é baseada em um roteador chamado RASoC, um soft-core para SoCs. Nesta dissertação será apresentada também uma rede heterogênea, baseada na rede SoCIN, e composta por dois tipos de roteadores – RASoC e Tonga. Estes roteadores visam diferentes objetivos: Rasoc alcança uma maior performance comparada ao Tonga, mas ocupa área consideravelmente maior. Potencialmente, uma NoC heterogênea otimizada pode ser desenvolvida combinando estes roteadores, procurando o melhor compromisso entre área e latência. Os modelos desenvolvidos permitem a estimativa de área e do desempenho das arquiteturas de comunicação propostas e são apresentados resultados de performance para algumas aplicações.

Implementação e avaliação de máquinas de comitê em um ambiente com múltiplos processadores embarcados em um único chip

The number of applications based on embedded systems grows significantly every year, even with the fact that embedded systems have restrictions, and simple processing units, the performance of these has improved every day. However the complexity of applications also increase, a better performance will always be necessary. So even such advances, there are cases, which an embedded system with a single unit of processing is not sufficient to achieve the information processing in real time. To improve the performance of these systems, an implementation with parallel processing can be used in more complex applications that require high performance. The idea is to move beyond applications that already use embedded systems, exploring the use of a set of units processing working together to implement an intelligent algorithm. The number of existing works in the areas of parallel processing, systems intelligent and embedded systems is wide. However works that link these three areas to solve any problem are reduced. In this context, this work aimed to use tools available for FPGA architectures, to develop a platform with multiple processors to use in pattern classification with artificial neural networks

Projeto de Sistemas Integrados de Propósito Geral Baseados em Redes em Chip Expandindo as Funcionalidades dos Roteadores para Execução de Operações: A plataforma IPNoSys

It bet on the next generation of computers as architecture with multiple processors and/or multicore processors. In this sense there are challenges related to features interconnection, operating frequency, the area on chip, power dissipation, performance and programmability. The mechanism of interconnection and communication it was considered ideal for this type of architecture are the networks-on-chip, due its scalability, reusability and intrinsic parallelism. The networks-on-chip communication is accomplished by transmitting packets that carry data and instructions that represent requests and responses between the processing elements interconnected by the network. The transmission of packets is accomplished as in a pipeline between the routers in the network, from source to destination of the communication, even allowing simultaneous communications between pairs of different sources and destinations. From this fact, it is proposed to transform the entire infrastructure communication of network-on-chip, using the routing mechanisms, arbitration and storage, in a parallel processing system for high performance. In this proposal, the packages are formed by instructions and data that represent the applications, which are executed on routers as well as they are transmitted, using the pipeline and parallel communication transmissions. In contrast, traditional processors are not used, but only single cores that control the access to memory. An implementation of this idea is called IPNoSys (Integrated Processing NoC System), which has an own programming model and a routing algorithm that guarantees the execution of all instructions in the packets, preventing situations of deadlock, livelock and starvation. This architecture provides mechanisms for input and output, interruption and operating system support. As proof of concept was developed a programming environment and a simulator for this architecture in SystemC, which allows configuration of various parameters and to obtain several results to evaluate it

Estudo da viabilidade do desenvolvimento de sistemas integrados baseados em redes em chip sem processadores: sistema IPNoSys

The increase of capacity to integrate transistors permitted to develop completed systems, with several components, in single chip, they are called SoC (System-on-Chip). However, the interconnection subsystem cans influence the scalability of SoCs, like buses, or can be an ad hoc solution, like bus hierarchy. Thus, the ideal interconnection subsystem to SoCs is the Network-on-Chip (NoC). The NoCs permit to use simultaneous point-to-point channels between components and they can be reused in other projects. However, the NoCs can raise the complexity of project, the area in chip and the dissipated power. Thus, it is necessary or to modify the way how to use them or to change the development paradigm. Thus, a system based on NoC is proposed, where the applications are described through packages and performed in each router between source and destination, without traditional processors. To perform applications, independent of number of instructions and of the NoC dimensions, it was developed the spiral complement algorithm, which finds other destination until all instructions has been performed. Therefore, the objective is to study the viability of development that system, denominated IPNoSys system. In this study, it was developed a tool in SystemC, using accurate cycle, to simulate the system that performs applications, which was implemented in a package description language, also developed to this study. Through the simulation tool, several result were obtained that could be used to evaluate the system performance. The methodology used to describe the application corresponds to transform the high level application in data-flow graph that become one or more packages. This methodology was used in three applications: a counter, DCT-2D and float add. The counter was used to evaluate a deadlock solution and to perform parallel application. The DCT was used to compare to STORM platform. Finally, the float add aimed to evaluate the efficiency of the software routine to perform a unimplemented hardware instruction. The results from simulation confirm the viability of development of IPNoSys system. They showed that is possible to perform application described in packages, sequentially or parallelly, without interruptions caused by deadlock, and also showed that the execution time of IPNoSys is more efficient than the STORM platform

Avaliação da execução de aplicações orientadas à dados na arquitetura de redes em chip IPNoSys

The increasing complexity of integrated circuits has boosted the development of communications architectures like Networks-on-Chip (NoCs), as an architecture; alternative for interconnection of Systems-on-Chip (SoC). Networks-on-Chip complain for component reuse, parallelism and scalability, enhancing reusability in projects of dedicated applications. In the literature, lots of proposals have been made, suggesting different configurations for networks-on-chip architectures. Among all networks-on-chip considered, the architecture of IPNoSys is a non conventional one, since it allows the execution of operations, while the communication process is performed. This study aims to evaluate the execution of data-flow based applications on IPNoSys, focusing on their adaptation against the design constraints. Data-flow based applications are characterized by the flowing of continuous stream of data, on which operations are executed. We expect that these type of applications can be improved when running on IPNoSys, because they have a programming model similar to the execution model of this network. By observing the behavior of these applications when running on IPNoSys, were performed changes in the execution model of the network IPNoSys, allowing the implementation of an instruction level parallelism. For these purposes, analysis of the implementations of dataflow applications were performed and compared

Implementação da técnica de software pipelining na rede em chip IPNoSyS

Alongside the advances of technologies, embedded systems are increasingly present in our everyday. Due to increasing demand for functionalities, many tasks are split among processors, requiring more efficient communication architectures, such as networks on chip (NoC). The NoCs are structures that have routers with channel point-to-point interconnect the cores of system on chip (SoC), providing communication. There are several networks on chip in the literature, each with its specific characteristics. Among these, for this work was chosen the Integrated Processing System NoC (IPNoSyS) as a network on chip with different characteristics compared to general NoCs, because their routing components also accumulate processing function, ie, units have functional able to execute instructions. With this new model, packets are processed and routed by the router architecture. This work aims at improving the performance of applications that have repetition, since these applications spend more time in their execution, which occurs through repeated execution of his instructions. Thus, this work proposes to optimize the runtime of these structures by employing a technique of instruction-level parallelism, in order to optimize the resources offered by the architecture. The applications are tested on a dedicated simulator and the results compared with the original version of the architecture, which in turn, implements only packet level parallelism

A label-free immunosensor based on recordable compact disk chip for early diagnostic of the dengue virus infection

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Fabricação de microcanais para integração de uma língua eletrônica em um sistema lab-on-a-chip

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)