Nikhil Gopalkrishnan

            PhD candidate, Duke CS

Research Overview

Self-assembly is a pervasive natural phenomenon that gives rise to complex structures and functions. It describes processes in which a disordered system of components form
organized structures as a consequence of specific, local interactions among the components themselves, without any external direction. Biological self-assembled systems, evolved over billions of years, are more intricate, more energy efficient and more functional than anything researchers have currently achieved at the nanoscale. A challenge for human designed physical self-assembled systems is to catch up with mother nature. DNA is an apt material to meet this challenge since it is programmable, chemically robust and predictable in its structure and interactions.

Publications

• The Tile Complexity of Linear Assemblies. Harish Chandran, Nikhil Gopalkrishnan and John Reif. Proceedings of the 36th International Colloquium on Automata, Languages and Programming (ICALP); July 5 - 12, 2009, Rhodes, Greece; pp. 235-253. PDF. (From Springer)

• Tile Complexity of Approximate Squares. Harish Chandran, Nikhil Gopalkrishnan and John Reif. Algorithmica, 2011. doi:10.1007/s00453-012-9620-z PDF. (From Springer)

• Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions. Harish Chandran, Nikhil Gopalkrishnan, Bernard Yurke, John Reif. Journal of the Royal Society Interface, published online before print (doi:10.1098/​rsif.2011.0819). PDF

•  Biomolecular Computing Systems - From Logic Systems to Smart Sensors and Actuators. Harish Chandran, Nikhil Gopalkrishnan, Sudhanshu Garg, and John Reif. Invited Chapter 13, Molecular and Biomolecular Information Processing (Editor: Evgeny Katz), Published by Wiley-VCH, to appear 2012.

• Localized Hybridization Circuits. Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips and John Reif. International Conference on DNA Computing and Molecular Programming, (DNA17), California Institute of Technology, Pasadina, California, Sept 19-23, 2011. Lecture Notes for Computer Science (LNCS), Springer-Verlag, LNCS, New York, (2011). PDF (From Springer)

• DNA NanoRobotics. Harish Chandran, Nikhil Gopalkrishnan, and John Reif. Invited Chapter in NanoRobotics, (edited by Constantinos Mavroidis), Springer, New York, NY, 2011.

• Self-assembled DNA Nanostructures and DNA Devices. John Reif, Harish Chandran, Nikhil Gopalkrishnan, and Thomas LaBean. Invited Chapter, Handbook of Nanofabrication (Edited by Stefano Cabrini and Satoshi Kawata), Taylor and Francis Group, New York, NY, ISBN 13:9781420090529, ISBN 10: 1420090526 (June 2011).

• High-Fidelity DNA Hybridization using Programmable Molecular DNA Devices. Nikhil Gopalkrishnan, Harish Chandran and John Reif. International Conference on DNA Computing and Molecular Programming (DNA16), Hong Kong University of Science and Technology. Hong Kong, China, June 14-17th, 2010. Lecture Notes for Computer Science (LNCS), Vol. 6516, Springer-Verlag, LNCS 6518, New York, (Feb 2011), pp 59-70. PDF. (From Springer)