Allocation heuristics and defragmentation measures for reconfigurable systems management

A novel technique is proposed for the management of a 2D reconfigurable device in order to get true hardware multitasking. We use a Vertex List Set to keep track of the free area boundary. This structure contains the best candidate locations for the task, and several heuristics are proposed to select one of them, based in fragmentation and adjacency. A Look-Ahead heuristic that anticipates the next known event is also proposed. A metric is used to estimate the fragmentation status of the FPGA, based on the number of holes and their shape. Defragmentation measures are taken when needed.     

Customization of an embedded RISC CPU with SIMD extensions for video encoding: A case study

This work presents a detailed case study in customizing a configurable, extensible, 32-bit RISC processor with vector/SIMD instruction extensions for the efficient execution of block-based video-coding algorithms utilizing a proprietary co-design environment. In addition to the default Full-Search motion estimation of the MPEG-2 Test Model 5, fourteen fast ME algorithms were implemented in both scalar and vector form. Results demonstrate a reduction of up to 68% in the dynamic instruction count of the full search-based encoder whereas the fast motion estimation algorithms achieved a reduction in instruction count of nearly 90%, both accelerated via three 128-bit vector/SIMD instructions when compared to the scalar, reference implementation of the standard. We address in detail the profiling, vectorization and the development of these vector instruction set extensions, discuss in depth the implementation of a parametric vector accelerator that implements these instructions and show the introduction of that accelerator into a 32-bit RISC processor pipeline, in a closely-coupled configuration.     

Interactions of DNA with graphene and sensing applications of graphene field-effect transistor devices: A review

Graphene field-effect transistors (GFET) have emerged as powerful detection platforms enabled by the advent of chemical vapor deposition (CVD) production of the unique atomically thin 2D material on a large scale. DNA aptamers, short target-specific oligonucleotides, are excellent sensor moieties for GFETs due to their strong affinity to graphene, relatively short chain-length, selectivity, and a high degree of analyte variability. However, the interaction between DNA and graphene is not fully understood, leading to questions about the structure of surface-bound DNA, including the morphology of DNA nanostructures and the nature of the electronic response seen from analyte binding. This review critically evaluates recent insights into the nature of the DNA graphene interaction and its affect on sensor viability for DNA, small molecules, and proteins with respect to previously established sensing methods. We first discuss the sorption of DNA to graphene to introduce the interactions and forces acting in DNA based GFET devices and how these forces can potentially affect the performance of increasingly popular DNA aptamers and even future DNA nanostructures as sensor substrates. Next, we discuss the novel use of GFETs to detect DNA and the underlying electronic phenomena that are typically used as benchmarks for characterizing the analyte response of these devices. Finally, we address the use of DNA aptamers to increase the selectivity of GFET sensors for small molecules and proteins and compare them with other, state of the art, detection methods.     

Bioanalytical applications of isothermal nucleic acid amplification techniques

The most popular in vitro nucleic acid amplification techniques like polymerase chain reaction (PCR) including real-time PCR are costly and require thermocycling, rendering them unsuitable for uses at point-of-care. Highly efficient in vitro nucleic acid amplification techniques using simple, portable and low-cost instruments are crucial in disease diagnosis, mutation detection and biodefense. Toward this goal, isothermal amplification techniques that represent a group of attractive in vitro nucleic acid amplification techniques for bioanalysis have been developed. Unlike PCR where polymerases are easily deactivated by thermally labile constituents in a sample, some of the isothermal nucleic acid amplification techniques, such as helicase-dependent amplification and nucleic acid sequence-based amplification, enable the detection of bioanalytes with much simplified protocols and with minimal sample preparations since the entire amplification processes are performed isothermally. This review focuses on the isothermal nucleic acid amplification techniques and their applications in bioanalytical chemistry. Starting off from their amplification mechanisms and significant properties, the adoption of isothermal amplification techniques in bioanalytical chemistry and their future perspectives are discussed. Representative examples illustrating the performance and advantages of each isothermal amplification technique are discussed along with some discussion on the advantages and disadvantages of each technique.     

Analytical devices based on light-emitting diodes – a review of the state-of-the-art

A general overview of the development of the uses of light-emitting diodes in analytical instrumentation is given. Fundamental aspects of light-emitting diodes, as far as relevant for this usage, are covered in the first part. The measurement of light intensity is also discussed, as this is an essential part of any device based on light-emitting diodes as well. In the second part, applications are discussed, which cover liquid and gas-phase absorbance measurements, flow-through detectors for chromatography and capillary electrophoresis, sensors, as well as some less often reported methods such as photoacoustic spectroscopy.     

Review of the role and methodology of high resolution approaches in aroma analysis

Analysis of the odour complexity in food and beverage products demands high resolution approaches for distinguishing individual aroma-impact compound(s), and for assessing their contribution to the global aroma of a sample. This paper aims to review current applications incorporating different advanced separation methodologies, and their roles in achieving high resolution aroma analysis. This includes prior low resolution gas chromatography–olfactometry (GC–O) with fractionation procedures using chemical manipulation, adsorption chromatography and ion exchange separation. Innovative multidimensional gas chromatography (MDGC) arrangements that are appropriately designed with olfactometry are of specific focus here. The revelation of resolved components using these integrated approaches provides significantly improved knowledge of aroma composition in samples.     

Signal amplification strategies for DNA and protein detection based on polymeric nanocomposites and polymerization: A review

Demand is increasing for ultrasensitive bioassays for disease diagnosis, environmental monitoring and other research areas. This requires novel signal amplification strategies to maximize the signal output. In this review, we focus on a series of significant signal amplification strategies based on polymeric nanocomposites and polymerization. Some common polymers are used as carriers to increase the local concentration of signal probes and/or biomolecules on their surfaces or in their interiors. Some polymers with special fluorescence and optical properties can efficiently transfer the excitation energy from a single site to the whole polymer backbone. This results in superior fluorescence signal amplification due to the resulting collective effort (integration of signal). Recent polymerization-based signal amplification strategies that employ atom transfer radical polymerization (ATRP) and photo-initiated polymerization are also summarized. Several distinctive applications of polymers in ultrasensitive bioanalysis are highlighted.     

Electrochemical sensors and biosensors based on redox polymer/carbon nanotube modified electrodes: A review

The aim of this review is to present the contributions to the development of electrochemical sensors and biosensors based on polyphenazine or polytriphenylmethane redox polymers together with carbon nanotubes (CNT) during recent years. Phenazine polymers have been widely used in analytical applications due to their inherent charge transport properties and electrocatalytic effects. At the same time, since the first report on a CNT-based sensor, their application in the electroanalytical chemistry field has demonstrated that the unique structure and properties of CNT are ideal for the design of electrochemical (bio)sensors. We describe here that the specific combination of phenazine/triphenylmethane polymers with CNT leads to an improved performance of the resulting sensing devices, because of their complementary electrical, electrochemical and mechanical properties, and also due to synergistic effects. The preparation of polymer/CNT modified electrodes will be presented together with their electrochemical and surface characterization, with emphasis on the contribution of each component on the overall properties of the modified electrodes. Their importance in analytical chemistry is demonstrated by the numerous applications based on polymer/CNT-driven electrocatalytic effects, and their analytical performance as (bio) sensors is discussed.