Keynote Speakers


Keynote 1

Rahul Sarpeshkar

Rahul Sarpeshkar

Thomas E. Kurtz Professor,
Dartmouth College, Hanover, NH, USA

Analog and Stochastic Computation in Living Cells and Supercomputing Chips

Abstract

Despite more than 15 years of research, synthetic circuits in living cells have been largely limited to a handful of digital logic gates and have not scaled. We show that one important reason for this failure to scale is an overemphasis on digital abstractions rather than on recognizing the true noisy, analog, and probabilistic nature of biological circuits. We show that synthetic and natural DNA, RNA, and protein circuits in cells must use analog, collective analog, probabilistic, and hybrid analog-digital computational approaches to function; otherwise, even relatively simple computations in cells will exceed energy, molecular-count, and cellular-resource budgets. Analog circuits in electronics and molecular circuits in cell biology are also deeply connected: There are astounding similarities between the equations that describe noisy electronic flow in sub-threshold transistors and the equations that describe noisy molecular flow in chemical reactions, both of which obey the laws of exponential thermodynamics. Based on these similarities, it is possible to take a principled approach to design circuits in living cells. For example, we have engineered logarithmic analog computation in living cells with less than three transcription factors, almost two orders of magnitude more efficient than prior digital approaches to create a 'bio-molecular slide rule'. In addition, highly computationally intensive noisy DNA-protein and protein-protein networks can be rapidly simulated in mixed-signal supercomputing chips that naturally capture their noisiness, dynamics, and non-modular interactions at lightning-fast speeds. Such an approach may enable large-scale design, analysis, simulation, and measurement of cells to be more precise and robust than it is today. To realize the promise of synthetic biology and systems biology for medicine, biotechnology, agriculture, and energy, we will need to go back to the future of computation and design and implement circuits via a collective analog approach like Nature does.

Short Biography

Rahul Sarpeshkar is currently the Thomas E. Kurtz Professor at Dartmouth, and a Professor in the departments of Engineering, Physics, Microbiology&Immunology, and Physiology&Neurobiology. His research creates novel wet DNA-protein circuits in living cells and also advanced dry nano-electronic circuits on silicon chips. His longstanding work on analog and biological computation and his most recent work have helped pioneer the field of analog synthetic biology. His work on a glucose fuel cell for medical implants was featured by Scientific American among 2012's 10 World Changing Ideas. He holds over 36 awarded patents and has authored more than 125 publications, including one that was featured on the cover of Nature. His recent book, Ultra Low Power Bioelectronics: Fundamentals, Biomedical Applications, and Bio-inspired Systems revealed the deep connections between analog transistor circuits and biochemical circuits. His group holds several first or best records in analog, bio-inspired, synthetic biology, medical device, ultra low power, and energy harvesting systems. His work has applications in implantable medical devices for the deaf, blind, and paralyzed and in biotechnology and medical applications that benefit from cellular engineering. He has received several awards including the NSF Career Award, the ONR Young Investigator Award, and the Packard Fellows Award. He received Bachelor's degrees in Electrical Engineering and Physics at MIT and a PhD at CalTech. Before he joined Dartmouth's faculty, he was a tenured professor at MIT, leading the analog circuits and biological systems group at the Research Lab of Electronics. Before joining MIT, he was a member of the technical staff of Bell Labs' division of biological computation in their physics department.



Keynote 2

Peng Yin

Peng Yin

Professor, Department of Systems Biology
Harvard Medical School
Cambridge, MA, USA

Molecular programming with DNA/RNA

Abstract

I will discuss my lab's research on engineering digitally programmable DNA/RNA nanostructures and their applications in imaging, sensing, and nanofabrication. We recently invented a general framework for programming the self-assembly of short synthetic nucleic acid strands into prescribed target shapes or demonstrating their prescribed dynamic behavior. Using short DNA strands, we demonstrated the modular construction of sophisticated nanostructures. Using reconfigurable DNA hairpins, we demonstrated diverse, dynamic behavior. By interfacing these nucleic acid nanostructures with functional modules, we are introducing digital programmability into diverse applications. (1) Barcoding and imaging life with DNA. Using programmable fluorescent DNA probes, we developed a highly multiplexed (10x), precisely quantitative (>90% precision), and ultra-high resolution (sub-5 nm) optical imaging method. (2) Probing and programming life with DNA/RNA. We constructed unprecedented robust and ultra-specific DNA probes for detecting single base changes in a single-stranded DNA/RNA target. We developed RNA nano-devices as de-novo-designed synthetic gene regulators with unprecedented wide dynamic range and orthogonality, and demonstrated their utility in living cells and on paper-based in vitro systems. (3) DNA-directed nano-foundries. We developed diverse strategies for producing inorganic materials with arbitrarily prescribed 2D (e.g. using graphene, silicon dioxides and 3D shapes (e.g. using silver, gold). See my lab's work at molecular-systems.net

Short Biography

Peng Yin is an Associate Professor of Systems Biology at Harvard Medical School and a Core Faculty Member at Wyss Institute for Biologically Inspired Engineering at Harvard University. He directs the Molecular Systems Lab at Harvard. His research interests lie at the interface of information science, molecular engineering, and biology. The current focus is to engineer information directed self-assembly of nucleic acid (DNA/RNA) structures and devices, and to exploit such systems to do useful molecular work. Such de novo designed systems are composed of small synthetic DNA/RNA monomers capable of conditional configuration change and can be programmed to self-assemble, move, and compute. They can serve as programmable controllers for the spatial and temporal arrangements of diverse functional molecules (e.g. fluorophores, proteins), with a wide range of applications in nano-fabrication, imaging, sensing, diagnostics, and therapeutics. He is a recipient of a 2010 NIH Director's New Innovator Award, a 2011 NSF CAREER Award, a 2011 DARPA Young Faculty Award, a 2011 ONR Young Investigator Program Award, a 2013 NIH Director's Transformative Research Award, a 2013 NSF Expedition in Computing Award, an inaugural 2014 ACS Synthetic Biology Young Investigator Award, a 2014 World Economic Forum Young Scientist Award, and a 2014 Finalist for Blavatnik National Award for Young Scientists. See his lab's work at molecular-systems.net



Keynote 3

Nader Engheta

Nader Engheta

Professor, Department of Electrical and Systems Engineering
University of Pennsylvania
Philadelphia, PA, USA

Let the Waves Do the Math!

Abstract

Recent development in condensed matter physics and nanoscience has made it possible to tailor materials with unusual parameters and characteristics. In my group, we have been exploring light-matter interaction in metamaterials and metastructures with extreme unusual parameters, investigating various features and potential applications of such platforms. As one of these directions, we have been studying how materials and structures can act as optical circuits at the nanoscale. By properly juxtaposing nanostructures with different material properties, we can design "circuits with light at the nanoscale." In this way, the alphabets of electronics and photonics become unified under the paradigm of optical metatronics. As one of the applications of such optical nanocircuits, we are investigating how materials and nanostructures can be chosen in order to manipulate electromagnetic and optical waves to achieve certain functionalities, such as performing mathematical operations on input wave's spatial profiles. Examples include designing structures that take spatial differentiation, spatial integration, spatial convolutions on the incoming waves. In this talk, we will present some of the features of optical metatronics and nanoscale analog computing using materials, discuss salient features of these structures, and forecast future directions and possibilities.
For further reading:

  • N. Engheta, "Circuits with light at nanoscales: Optical nanocircuits inspired by metamaterials," Science, 317, 1698-1702 (2007);
  • A. Silva, F. Monticone, G. Castaldi, V. Galdi, A. Alu, and N. Engheta, "Performing mathematical operations with metamaterials," Science, 343, 160-163 (2014);
  • Y. Sun, B. Edwards, A. Alu, and N. Engheta, "Experimental Realization of Optical Lumped Nanocircuit Elements at Infrared Wavelengths," Nature Materials, 11, 208-212 (2012);
  • C. Della Giovampaola and N. Engheta, "Digital Metamaterials," Nature Materials, 13, 1115-1121 (2014)


Short Biography

Nader Engheta is the H. Nedwill Ramsey Professor at the University of Pennsylvania in Philadelphia, with affiliations in the Departments of Electrical and Systems Engineering, Physics and Astronomy, Bioengineering, and Materials Science and Engineering. He received his B.S. degree from the University of Tehran, and his M.S and Ph.D. degrees from Caltech. Selected as one of the Scientific American Magazine 50 Leaders in Science and Technology in 2006 for developing the concept of optical lumped nanocircuits, he is a Guggenheim Fellow, an IEEE Third Millennium Medalist, a Fellow of IEEE, American Physical Society (APS), Optical Society of America (OSA), American Association for the Advancement of Science (AAAS), SPIE, and Materials Research Society (MRS), and the recipient of several awards for his research including 2015 Gold Medal from SPIE (International Society for Optics and Photonics), 2014 Balthasar van der Pol Gold Medal from the International Union of Radio Science (URSI), 2013 Benjamin Franklin Key Award, 2013 Inaugural SINA Award in Engineering, 2012 IEEE Electromagnetics Award, 2008 George H. Heilmeier Award for Excellence in Research, the Fulbright Naples Chair Award, NSF Presidential Young Investigator award, the UPS Foundation Distinguished Educator term Chair, and several teaching awards including the Christian F. and Mary R. Lindback Foundation Award, S. Reid Warren, Jr. Award and W. M. Keck Foundation Award. His current research activities span a broad range of areas including nanophotonics, metamaterials, nano-scale optics, graphene optics, imaging and sensing inspired by eyes of animal species, optical nanoengineering, microwave and optical antennas, and engineering and physics of fields and waves. He has co-edited (with R. W. Ziolkowski) the book entitled "Metamaterials: Physics and Engineering Explorations" by Wiley-IEEE Press, 2006. He was the Chair of the Gordon Research Conference on Plasmonics in June 2012.

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