Digital Microfluidic Biochips: From Manipulating Droplets to A Cyberphysical System for Quantitative Gene-Expression Analysis
Abstract:
Advances in microfluidics have led to the emergence of biochips for automating laboratory procedures in molecular biology. These devices enable the precise control of nanoliter volumes of biochemical samples and reagents. As a result, non-traditional biomedical applications and markets (e.g., high-throughout DNA sequencing, portable and point-of-care clinical diagnostics, protein crystallization for drug discovery), and fundamentally new uses are opening up for ICs and systems.
This lecture will first introduce electrowetting-based digital microfludic biochips and provide an overview of market drivers such as immunoassays and DNA sequencing. The audience will next learn about design automation and reconfiguration aspects of microfluidic biochips. Synthesis tools will be described to map assay protocols from the lab bench to a droplet-based microfluidic platform and generate an optimized schedule of bioassay operations, the binding of assay operations to functional units, and the layout and droplet-flow paths for the biochip. The role of the digital microfluidic platform as a “programmable and reconfigurable processor” for biochemical applications will be highlighted. The speaker will describe dynamic adaptation of bioassays through cyberphysical system integration and sensor-driven on-chip error recovery.
Finally, the speaker will highlight recent advances in utilizing cyberphysical integration for quantitative gene-expression analysis. This framework is based on a real-time resource-allocation algorithm that responds promptly to decisions about the protocol flow received from a firmware layer. Results will be presented on how this adaptive framework efficiently utilizes on-chip resources to reduce time-to-result without sacrificing the chip’s lifetime.
speaker：
KRISHNENDU CHAKRABARTY
Full Professor in Duke University
ACM Fellow & IEEE Fellow
Krishnendu Chakrabarty is now the William H. Younger Distinguished Professor of Engineering in the Department of Electrical and Computer Engineering and Professor of Computer Science at Duke University. He also serves as Director of Graduate Studies for Electrical and Computer Engineering. Prof. Chakrabarty is a recipient of the National Science Foundation Early Faculty (CAREER) award, the Office of Naval Research Young Investigator award, the Humboldt Research Award from the Alexander von Humboldt Foundation, Germany, the IEEE Transactions on CAD Donald O. Pederson Best Paper award (2015), and 11 best paper awards at major IEEE conferences. He is also a recipient of the IEEE Computer Society Technical Achievement Award (2015) and the Distinguished Alumnus Award from the Indian Institute of Technology, Kharagpur (2014). He is a Research Ambassador of the University of Bremen (Germany). He is also a Hans Fischer Senior Fellow (named after Nobel Laureate Prof. Hans Fischer) at the Institute for Advanced Studies, Technical University of Munich, Germany.
Prof. Chakrabarty’s current research projects include: testing and design-for-testability of integrated circuits; digital microfluidics, biochips, and cyberphysical systems; optimization of enterprise systems and smart manufacturing. He has authored 17 books on these topics (with one more book in press), published over 560 papers in journals and refereed conference proceedings, and given over 260 invited, keynote, and plenary talks. He has also presented 50 tutorials at major international conferences. Prof. Chakrabarty is a Fellow of ACM, a Fellow of IEEE, and a Golden Core Member of the IEEE Computer Society. He holds seven US patents, with several patents pending. He was a 2009 Invitational Fellow of the Japan Society for the Promotion of Science (JSPS). He is a recipient of the 2008 Duke University Graduate School Dean’s Award for excellence in mentoring, and the 2010 Capers and Marion McDonald Award for Excellence in Mentoring and Advising, Pratt School of Engineering, Duke University. He has served as a Distinguished Visitor of the IEEE Computer Society (2005-2007, 2010-2012), and as a Distinguished Lecturer of the IEEE Circuits and Systems Society (2006-2007, 2012-2013). Currently he serves as an ACM Distinguished Speaker.
Prof. Chakrabarty served as the Editor-in-Chief of IEEE Design & Test of Computers during 2010-2012 and ACM Journal on Emerging Technologies in Computing Systems during 2010-2015. Currently he serves as the Editor-in-Chief of IEEE Transactions on VLSI Systems. He is also an Associate Editor of IEEE Transactions on Computers, IEEE Transactions on Biomedical Circuits and Systems, IEEE Transactions on Multiscale Computing Systems, and ACM Transactions on Design Automation of Electronic Systems. He serves as an Editor of the Journal of Electronic Testing: Theory and Applications (JETTA). In the recent past, he has served as Associate Editor of IEEE Transactions on VLSI Systems (2005-2009), IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (2001-2013), IEEE Transactions on Circuits and Systems I (2005-2006), and IEEE Transactions on Circuits and Systems II (2010-2013).
