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Tsung-Yi Ho Region - 10

Prof. Tsung-Yi Ho
National Cheng Kung University
Department of Computer Science and Information Engineering
No. 1, University Rd., Tainan City
Phone: +886-6-2757575 ext. 62552
Fax: +886-6-2747076
Email: tyho@csie.ncku.edu.tw

Tsung-Yi Ho received his Ph.D. degrees in Electrical Engineering from
National Taiwan University, Taipei, Taiwan, ROC, in 2005. Since 2007,
he has been with the Department of Computer Science and Information
Engineering, National Cheng Kung University, Tainan, Taiwan, ROC,
where he is currently an Associate Professor. His research interests
include design automation for microfluidic biochips and nanometer
integrated circuits. He has published several papers in top journals
and conferences such as IEEE TCAD, ACM TODAES, ACM/IEEE DAC, IEEE/ACM
ICCAD, ACM ISPD, and etc. He was the recipient of many research
awards, such as Dr. Wu Ta-You Memorial Award of National Science
Council (NSC) of Taiwan (the most prestigious award from NSC for
junior researchers), Distinguished Young Scholar Award of Taiwan IC
Design Society, ACM Taipei Chapter Young Researcher Award, IEEE Tainan
Chapter Gold Member Award, the Invitational Fellowship of the Japan
Society for the Promotion of Science (JSPS), Japan, and the Humboldt
Research Fellowship from the Alexander von Humboldt Foundation,
Germany. He is a senior member of IEEE.

More info about Prof. Ho can be found at http://eda.csie.ncku.edu.tw/~tyho

Digital Microfluidic Biochips: Towards Hardware/Software Co-Design and
Cyberphysical System Integration

Advances in droplet-based digital microfluidic biochips (DMFBs) have
led to the emergence of biochips for automating laboratory procedures
in biochemistry and molecular biology. These devices enable the
precise control of microliter of nanoliter volumes of biochemical
samples and reagents. They combine electronics with biology, and
integrate various bioassay operations, such as sample preparation,
analysis, separation, and detection. To meet the challenges of
increasing design complexity and precision, the interplay between
hardware and software through sensor-based cyberphysical integration
will be involved to build DMFBs effectively. This talk offers
attendees an opportunity to bridge the semiconductor ICs/system
industry with the biomedical and pharmaceutical industries. The talk
will first describe emerging applications in biology and biochemistry
that can benefit from advances in electronic "biochips". The presenter
will next describe technology platforms for accomplishing
"biochemistry on a chip", and introduce the audience to microarrays
and fluidic actuation methods based on microfluidics. The
droplet-based "digital" microfluidic platform based on electrowetting
will be described in considerable detail. Next, the presenter will
describe fabrication techniques for digital microfluidic biochips,
followed by computer-aided design, design-for-testability,
cyberphysical integration, and reconfiguration aspects of chip/system
design. Synthesis algorithms and methods will be presented to map
behavioral descriptions to a digital microfluidic platform, and
generate an optimized schedule of bioassay operations, chip layout,
and droplet-flow paths. In this way, the audience will see how a
"biochip compiler" can translate protocol descriptions provided by an
end user (e.g., a chemist or a nurse at a doctor's clinic) to a set of
optimized and executable fluidic instructions that will run on the
underlying digital microfluidic platform.

Top-Down Synthesis for Flow-Based Microfluidic Biochips

As the design complexity rapidly increases, the manufacture and the
biochemical analysis of flow-based microfluidic biochip become more
complicated. According to recent study, the biochips can now use more
than 25,000 valves and about a million features to run 9,216 parallel
polymerase chain reactions. Moreover, the number of mechanical valves
per square inch for flow-based microfluidic biochips has grown
exponentially and four times faster than the reflection of Moore's
Law. Although the scale for flow-based microfluidic biochips is
enlarging and the total amount of the valves fabricated on a chip are
also growing significantly, computer-aided design (CAD) tools are
still in their infancy today. Designers are using bottom-up
full-custom design approaches involving multiple non-automated steps
to manually adjust the components and the connection to satisfy the
steps of desired biochemical applications. As a result, the
development of explicit design rules and strategies allowing modular
top-down synthesis methodologies are needed, in order to provide the
same level of CAD support for the biochip designer as the one that are
currently done for the semiconductor industry. However, for
miniaturization, integration, automation and parallelization of
biochemical processes, a flow-based microfluidic biochip needs a lot
of chip-integrated micro-valves, i.e. the basic unit of fluid-handling
functionality, to manipulate the fluid flow for biochemical
applications. Moreover, frequent switching of micro-valves may cause
power consumption and even reliability problems. To minimize the
valve-switching activities, this talk presents a top-down synthesis
methodology based on breadth first search (BFS) and minimum cost
maximum flow (MCMF) to synthesize the flow-based microfluidic biochip.
The experimental results show that our methodology not only makes
significant reduction of valve-switching activities but also
diminishes the application completion time for both real-life
applications and a set of synthetic benchmarks.