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收集所有交通大學研究人員與學生個人或團體所發表之各項學術著作，涵蓋期刊論文、教師專書、學位論文等項。;;Collections of Publications of NCTU Researchers and Students Like Journal Papers and Thesis.

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    Storage-Aware Algorithms for Dilution and Mixture Preparation With Flow-Based Lab-on-Chip
    (2020-04-01)
    Bhattacharjee, Sukanta
    ;
    Wille, Robert
    ;
    Huang, Juinn-Dar
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    Bhattacharya, Bhargab B.
    ;
    電子工程學系及電子研究所
    Lab-on-chip (LoC) technology has emerged as one of the major driving forces behind the recent surge in biochemical protocol automation. Dilution and mixture preparation with fluids in a desired ratio, constitute basic steps in sample preparation for which several LoC-based architectures and algorithms are known. The optimization of cost and time for such protocols requires proper sequencing of fluidic mix-and-split steps, and storage-units for holding intermediate-fluids to be reused in the later steps. However, practical design constraints often limit the amount of on-chip storage in microfluidic LoC architectures and thus can badly affect the performance of the algorithms. Consequently, results generated by previous work may not be useful (in the case they require more storage-units than available) or more expensive than necessary (in the case when storage-units are available but not used, e.g., to further reduce the number of mix/split operations or reactant-cost). In this paper, we propose new algorithms for dilution and mixing with continuous-flow-based LoCs that explicitly take care of storage constraints while optimizing reactant-cost and time of sample preparation. We present a symbolic formulation of the problem that captures the degree of freedom in algorithmic steps satisfying the specified storage constraints. Solvers based on Boolean satisfiability are used to achieve the optimization goals. The experimental results show the efficiency and effectiveness of the solution as well as a variety of applications where the proposed methods would prove beneficial.
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    Design and Optimization of a Cyberphysical Digital-Microfluidic Biochip for the Polymerase Chain Reaction
    (2015-01-01)
    Luo, Yan
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    Bhattacharya, Bhargab B.
    ;
    Ho, Tsung-Yi
    ;
    Chakrabarty, Krishnendu
    ;
    資訊工程學系
    The amount of DNA strands available in a biological sample is a major limitation for many genomic bioanalyses. To amplify the traces of DNA strands, polymerase chain reaction (PCR) is widely used for conducting subsequent experiments. Compared to conventional instruments and analyzers, the execution of PCR on a digital microfluidic biochip (DMFB) can achieve short time-to-results, low reagent consumption, rapid heating/cooling rates, and high integration of multiple processing modules. However, the PCR biochip design methods in the literature are oblivious to the inherent randomness and complexity of bioanalyses, and they do not consider the interference among the neighboring devices and the cost of droplet transportation. We present an integrated design solution to optimize the complete PCR procedure, including: 1) DNA amplification and termination control; 2) resource placement that satisfies proximity constraints; and 3) droplet transportation. Based on the sensor feedback data, a statistical model is developed to optimize and control the DNA amplification sequence in real-time on a cyberphysical biochip. Next, we present a geometric algorithm for avoiding device interference and for reducing droplet routing cost. A novel optical sensing system is deployed based on the physical visibility of droplets. Simulation results for three laboratory protocols demonstrate that the proposed design method results in a compact layout and produces an execution sequence for efficient control of PCR operations on a cyberphysical DMFB.