Transport or Store? Synthesizing Flow-based Microfluidic Biochips using Distributed Channel Storage

Flow-based microfluidic biochips have attracted much atten- tion in the EDA community due to their miniaturized size and execution efficiency. Previous research, however, still follows the traditional computing model with a dedicated storage unit, which actually becomes a bottleneck of the performance of bio- chips. In this paper, we propose the first architectural synthe- sis framework considering distributed storage constructed tem- porarily from transportation channels to cache fluid samples. Since distributed storage can be accessed more efficiently than a dedicated storage unit and channels can switch between the roles of transportation and storage easily, biochips with this dis- tributed computing architecture can achieve a higher execution efficiency even with fewer resources. Experimental results con- firm that the execution efficiency of a bioassay can be improved by up to 28% while the number of valves in the biochip can be reduced effectively.Comment: ACM/IEEE Design Automation Conference (DAC), June 201

Testing Microfluidic Fully Programmable Valve Arrays (FPVAs)

Fully Programmable Valve Array (FPVA) has emerged as a new architecture for the next-generation flow-based microfluidic biochips. This 2D-array consists of regularly-arranged valves, which can be dynamically configured by users to realize microfluidic devices of different shapes and sizes as well as interconnections. Additionally, the regularity of the underlying structure renders FPVAs easier to integrate on a tiny chip. However, these arrays may suffer from various manufacturing defects such as blockage and leakage in control and flow channels. Unfortunately, no efficient method is yet known for testing such a general-purpose architecture. In this paper, we present a novel formulation using the concept of flow paths and cut-sets, and describe an ILP-based hierarchical strategy for generating compact test sets that can detect multiple faults in FPVAs. Simulation results demonstrate the efficacy of the proposed method in detecting manufacturing faults with only a small number of test vectors.Comment: Design, Automation and Test in Europe (DATE), March 201

Plasmonic Cavities for Enhanced Spotaneous Emission

The modification of spontaneous emission, i.e. the Purcell effect, with optical cavities has been highly studied over the past 20 years as one of the most important goals for cavity quantum electrodynamics (cQED). The recent development of using surface plasmon resonances to concentrate optical field into sub-wavelength scale further extended cQED research of into a new regime. However, although metallic reflectors are used in some of the earliest demonstrations of cQED, the use of metals is not preferable in high Q optical cavities due to the lossy nature of metals. The presence of metals near an optical emitter also strongly alters its radiation dynamics. As a result, the development of plasmonic cavities brings not only new opportunities but also new problems and challenges. In this thesis we describe four different plasmonic cavity designs along with optical simulations and measurements on them to demonstrate: large spontaneous emission enhancement, controlled mode tuning, and control of the plasmonic band-gap and resonances of high-Q plasmonic cavities for coupling to specific emitters. We hope that our work can guide and inspire researchers who are moving from traditional cavity designs to novel plasmonic devices, helping them to establish design concepts, fabrication criteria, and baselines for characterizing these devices.Engineering and Applied Science

4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell-derived intestinal organoids.

New methods in stem cell 3D organoid tissue culture, advanced imaging, and big data image analytics now allow tissue-scale 4D cell biology, but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high-content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome-edited human embryonic stem cells, which were differentiated into hESC-derived intestinal epithelial organoids. Lattice light-sheet imaging with adaptive optics (AO-LLSM) allowed us to image large volumes of these organoids (70 × 60 × 40 µm xyz) at 5.7 s/frame. We developed an open-source data analysis package termed pyLattice to process the resulting large (∼60 Gb) movie data sets and to track clathrin-mediated endocytosis (CME) events. CME tracks could be recorded from ∼35 cells at a time, resulting in ∼4000 processed tracks per movie. On the basis of their localization in the organoid, we classified CME tracks into apical, lateral, and basal events and found that CME dynamics is similar for all three classes, despite reported differences in membrane tension. pyLattice coupled with AO-LLSM makes possible quantitative high temporal and spatial resolution analysis of subcellular events within tissues

Controlled mode tuning in 1-D ‘RIM’ plasmonic crystal trench cavities probed with coupled optical emitters

We present a design of plasmonic cavities that consists of two sets of 1-D plasmonic crystal reflectors on a plasmonic trench waveguide. A 'reverse image mold' (RIM) technique was developed to pattern high-resolution silver trenches and to embed emitters at the cavity field maximum, and FDTD simulations were performed to analyze the frequency response of the fabricated devices. Distinct cavity modes were observed from the photoluminescence spectra of the organic dye embedded within these cavities. The cavity geometry facilitates tuning of the modes through a change in cavity dimensions. Both the design and the fabrication technique presented could be extended to making trench waveguide-based plasmonic devices and circuits.Engineering and Applied Science

Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution, without inducing undue stress on either. We combined lattice light-sheet microscopy with adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments

Tri-layer self-aligned structure indium gallium zinc oxide thin film transistor with optical synaptic plasticity

Since the 1950s, computer computing has been governed by the von Neumann architecture, which allows data to be transmitted across the processor and memory for computation. Nowadays, the demand for large amounts of information transmission has limited the processing speed by the memory bandwidth and generated higher power consumption. The Human brain can perform high-speed operation, store and calculate as one, so the human neuromorphic computation is the next-generation architecture to solve the “von Neumann bottleneck” [1- 2]. In this work, we have successfully developed tri-layer self-aligned structure indium gallium oxide (IGZO) thinfilm transistors (TFTs) with optical-synaptic plasticity. The channel conductance of IGZO TFTs would be modulated after the pulse voltage input from gate electrode. Please click Download on the upper right corner to see the full abstract