21 research outputs found
Chemocapacitance response simulation through polymer swelling and capacitor modeling
No full textAbstractA methodology for the prediction of chemocapacitor response due to the sorption of analyte without the need for fabrication of the actual devices is introduced. The methodology is based on experimental measurement of volume fraction due to sorption of the analyte through reflectance measurements and electromagnetic modeling for the InterDigitated Electrode (IDE) capacitor. The volume fraction and the capacitance of the device are coupled through the use of Clausius-Mossotti equation for the calculation of dielectric constant of sorbed polymeric film resulting in the prediction of the capacitance change due to the sorption of the analyte
Molecular dynamics simulation of gel formation and acid diffusion in negative tone chemically amplified resists
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Evaluation of DNA scaffolding techniques using PacBio long reads
No full textThe goal of this study was to dive into the novel techniques associated with the use of the available Third Generation DNA Sequencing (TGS) platform, PacBio. This 3-year old technology sounded promising right from the beginning but its groundbreaking attributes, like length and error content, required unconventional handling to yield worthwhile results. To date, only a handful of tools exist that operate on TGS datasets compared to the enormous mass of Second Generation Sequencing (SGS) assemblers out there. In order to efficiently utilize this innovative technology, we need to familiarize ourselves with its characteristics and study the mistakes the existing tools made. To achieve this, a simulated environment was created aiming to comprehensively evaluate two popular hybrid scaffolders (AHA, SSPACE-LongRead) and through that, gain knowledge on the impact of PacBio dataset properties on scaffolding. The evaluation was not limited to contiguity performance (N50/90, etc.) but also examined the accuracy of the results.Three different reference genomes (ecoli, arabidopsis and human) were used for the evaluation and multiple runs were executed for statistical purposes. Apart from the simulated experiments, the capabilities of both tools were also tested on a real dataset, cyprinus carpio (carp fish). Comparison-wise, each tool thrived in distinct situations with SSPACE-LongRead demonstrating better contiguity capabilities (~60% longer N50) and shorter execution time (3–14x faster) whereas AHA was the most accurate one (up to 4x less incorrect joins). PacBio dataset coverage and error rate displayed inconsiderable effect on the result on small genome scaffolding but more pronounced on complex ones. Surprisingly, random features of PacBio sequencing, like length distribution and position of error, had a dominant effect on the performance. Finally, on the carp dataset experiments, AHA achieved a 6x increase in N50 and maximum length while SSPACE-LongRead failed to finish the execution (scaffolded one fourth of the genome). It managed, nevertheless, to produce scaffolds with a maximum length of 646Kbp, compared to 501Kbp of AHA.Computer EngineeringDepartment of Electrical EngineeringElectrical Engineering, Mathematics and Computer Scienc
Modelling and evaluation of a thermal microfluidic sensor fabricated on plastic substrate
No full textAbstractBoth the simulation and the experimental evaluation of a thermal microfluidic flow sensor are presented in this work. The sensor was evaluated in the calorimetric principle of operation with water as the test liquid. The simulation of the sensor operation was performed into the framework of Comsol® software package. Various combinations of microchannel geometries were tested with different input flow rate values. The operational parameters of the device were simulated by 3D models. The dominant operation parameter was determined to be the distance of the upstream-downstream sensing elements to the heater, the effect of which was theoretically extracted and experimentally verified
Fractals and device performance variability: The key role of roughness in micro and nanofabrication
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Performance simulation, realization and evaluation of capacitive sensor arrays for the real time detection of volatile organic compounds
No full textCapacitive-type gas sensors rely on changes in the dielectric properties of the sensing polymeric layer due to absorption of Volatile Organic Compounds (VOCs) or moisture. They are promising devices in terms of ease and low cost of fabrication, reversibility and the wide range of sensing material choice. In the present work, the aim is to explore the fabrication issues of the InterDigitated Electrodes (IDE) through a generic simulation model for the prediction of the capacitance of various IDE structures. Based on the simulation results, an IDE layout was selected for the realization and evaluation of chemcapacitor arrays in the presence of different humidity levels and low concentrations of VOCs with dielectric constant close to those of polymers. The extracted results will be further exploited for the fabrication optimization of an InterDigitated Capacitor (IDC) layout with increased selectivity and sensitivity in specific applications. © 2011 Elsevier B.V. All rights reserved
E-beam proximity correction for negative tone chemically amplified resists taking into account post-bake effects
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