Browsing by Author "Zhong, Zhanwei"
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Item Open Access Design, Optimization and Test Methods for Robust Digital Microfluidic Biochips(2020) Zhong, ZhanweiMicrofluidic biochips are now being used for biochemical applications such as high-throughput DNA sequencing, point-of-care clinical diagnostics, and immunoassays. In particular, digital microfluidic biochips (DMFBs) are especially promising. They manipulate liquid as discrete droplets of nanoliter or picoliter volumes based on the principle of electrowetting-on-dielectric under voltage-based electrode actuation. DMFBs have been commercially adopted for sample preparation and clinical diagnostics. Techniques have also been developed for high-level synthesis, module placement, and droplet routing.
However, reliability is a major concern in the use of DMFBs for laboratory protocols. In addition to manufacturing defects and imperfections, faults can also arise during a bioassay. For example, excessive or prolonged actuation voltage may lead to electrode breakdown and charge trapping, and DNA fouling may lead to the malfunction of electrodes. Faults may eventually result in errors in droplet operations. If an unexpected error appears during an experiment, the outcome of the experiment will be incorrect. The repetition of an experiment leads to wastage of valuable reagents and time.
Therefore, it is necessary to ensure the correctness of the hardware and bioassay execution on the biochip. In this thesis, we focus on three types of reliability: biochip testing, error/fault recovery, and fault-tolerant synthesis. First, when a biochip is fabricated, defects might occur in parts of the biochip. Therefore, our objective is to develop biochip testing methods to detect and locate faults. Second, to faults that appear during droplet operation or in the hardware, we develop error-recovery procedures and redundancy solutions. Finally, we develop fault-tolerant synthesis techniques so that even if faults occur during droplet operations (e.g., unbalance splitting), the bioassay can proceed unimpeded. The proposed solutions are applied to two new types of biochip platforms, namely micro-electrode-dot-array (MEDA) and digital acoustofluidics.
Item Open Access Efficient Regulation of Synthetic Biocircuits Using Droplet-Aliquot Operations on MEDA BiochipsIbrahim, mohamed; Zhong, Zhanwei; Bhattacharya, Bhargab B; Chakrabarty, KrishnenduItem Open Access Hardware Design and Fault-Tolerant Synthesis for Digital Acoustofluidic Biochips.(IEEE transactions on biomedical circuits and systems, 2020-10) Zhong, Zhanwei; Zhu, Haodong; Zhang, Peiran; Morizio, James; Huang, Tony Jun; Chakrabarty, KrishnenduA digital microfluidic biochip (DMB) is an attractive platform for automating laboratory procedures in microbiology. To overcome the problem of cross-contamination due to fouling of the electrode surface in traditional DMBs, a contactless liquid-handling biochip technology, referred to as acoustofluidics, has recently been proposed. A major challenge in operating this platform is the need for a control signal of frequency 24 MHz and voltage range ±10/±20 V to activate the IDT units in the biochip. In this paper, we present a hardware design that can efficiently activate/de-activated each IDT, and can fully automate an bio-protocol. We also present a fault-tolerant synthesis technique that allows us to automatically map biomolecular protocols to acoustofluidic biochips. We develop and experimentally validate a velocity model, and use it to guide co-optimization for operation scheduling, module placement, and droplet routing in the presence of IDT faults. Simulation results demonstrate the effectiveness of the proposed synthesis method. Our results are expected to open new research directions on design automation of digital acoustofluidic biochips.Item Open Access Robust Fault-Recovery Method for MEDA Biochips Using an IJTAG Network(IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems, 2020-02-25) Zhong, Zhanwei; Chakrabarty, Krishnendu