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Dunbar receives award to study biomolecular control

Dunbar's research uses real-time control to extend the capabilities of nanopore systems
Dunbar's research uses real-time control to extend the capabilities of nanopore systems
Monday, May 18, 2009
Computer Engineering

William Dunbar, assistant professor of computer engineering, has been awarded a National Science Foundation CAREER grant. The prestigious NSF early career development program awards 5-year research grants to the nation’s most promising faculty.

For Professor Dunbar, this grant represents the next stage of a deliberative integration of biomolecular science with his work on control, the area of applied engineering concerning the ability of technology, mathematics, and algorithms to affect the physical world in predictable and desirable ways. In 2005, Dunbar received a similarly prestigious National Institutes of Health Mentored Quantitative Research Development Award (K25), a five-year retraining program focused on enabling exceptional researchers in mathematical disciplines to gain the biological and biomedical training necessary to pursue innovative interdisciplinary work.

 “It’s really a great honor, particularly to have NSF and my colleagues from control recognize and support the transition I am trying to make in research at the interface of control and biomolecular engineering,” Dunbar says, continuing “The CAREER grant will support some very exciting projects for graduate students. In particular, we plan to measure and manipulate individual enzymes bound to DNA. In clinical setting, this could make it possible for scientists to quantitatively compare, and thus discern between, healthy and aberrant/mutated enzymes at the single molecule level.”

The research will study the measurement, modeling and control of molecular motors above a nanopore, an opening designed to allow only a single strand of double-stranded DNA to pass through. Dunbar’s prior work has been an instrumental part of the collaboration with biomolecular engineering professors David Deamer and Mark Akeson to unlock the potential of this new technology, detailed in a Currents article. In his work, Dunbar developed a method of using active voltage control to regulate a single DNA in a nanopore for repeated binding and dissociation of individual enzymes above the nanopore. This system enables the extended analysis of the DNA strand, and as the system is continues to be improved, will enable previously unseen accuracy in DNA molecular analysis within an easily-replicated experimental setup. 

Due to its exceptional promise, in August 2008, Oxford Nanopore licensed the UCSC technology, and in January 2009, Oxford Nanopore created a strategic alliance with Illumina to develop the new technology into low-cost sequencing systems. The system, which is planned to determine the sequence of a person’s DNA with a simple lab test costing less than $1000, will revolutionize medicine, enabling routine screenings and personalized drug selection based on test results.  Professors Akeson and Deamer are members of the Oxford Nanopore technical advisory board.

Professor Dunbar’s CAREER grant includes a focus on education. Dunbar will continue his efforts to provide a first-quarter introduction to the power of mathematics within engineering though his course CMPE8: Robot Automation. The class introduces control algorithms with a sole prerequisite of high school algebra. This strategy ensures students continue their excitement about robotics and engineering throughout their study, rather than drown in a torrent of foundational material. He will also launch a new graduate course on the role of feedback control in single molecule instrumentation, for computer and electrical engineering and bioengineering students.

Professor Dunbar received the B.S. degree in engineering science and mechanics from Virginia Tech in 1997, the M.S. degree in applied mechanics and engineering science from UC San Diego in 1999, and the Ph.D. in control and dynamical systems from Caltech in 2004. He has been an assistant professor of computer engineering at UCSC since 2004. Prof. Dunbar's research projects include distributed coordination algorithms in air traffic control (funded by NASA), and feedback control of single molecules in a nanopore for biophysical measurement and modeling (funded by the NSF CAREER grant and the NIH K25 retraining grant). He is a consultant for Toyota (TEMA), and for Australo Limited, a New Zealand-based biotechnology company.