Research

I have been an academic researcher for the past six years in various fields of computer science and natural science at three major research institutions: WARFT, India, Duke University, USA and Microsoft Research Cambridge, UK. I have worked with large and small teams in various projects in computer architecture, supercomputing, benchmarking, computational neuroscience, algorithms, algorithmic self-assembly, DNA self-assembly and DNA nanoscience. At Duke, I have been working on theory, simulations and experiments on DNA nanoscience. The self-assembly of DNA strands can be utilized in the construction nanoscale objects and for precise control of nanoscale phenomenon. I develop formal models of self-assembly and seek to answer questions related to the number of strands required to build to a particular shape or perform a particular action. This involves mathematical modeling and stochastic analysis of complex systems. I also design DNA hybridization based systems to achieve computation and other useful behavior such as amplification, detection etc. I simulate these systems using various softwares and finally perform wet lab experiments on systems that show most promise. You can download a more detailed research statement here.

Publications

Book Chapters

[1.] Self-assembled DNA Nanostructures and DNA Devices, Nanofabrication Handbook, Taylor and Francis 2012, with Nikhil Gopalkrishnan, Thom LaBean and John Reif
[2.] DNA Nanorobotics, Nanorobotics, Springer 2012, with Nikhil Gopalkrishnan and John Reif
[3.] Biomolecular Computing Systems, Molecular and Supramolecular Information Processing: From Molecular Switches to Logic Systems, Wiley 2012, with Sudhanshu Garg, Nikhil Gopalkrishnan and John Reif

Journal Papers

[4.] Tile Complexity of Approximate Squares, Algorithmica, with Nikhil Gopalkrishnan and John Reif
[5.] Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions, Journal of Royal Society Interface, 2012, with Nikhil Gopalkrishnan, Bernard Yurke and John Reif Press Coverage

Conference Papers

[6.] Localized Hybridization Circuits, DNA17, with Nikhil Gopalkrishnan, Andrew Phillips and John Reif
[7.] High-Fidelity DNA Hybridization using Programmable Molecular DNA Devices, DNA16, with Nikhil Gopalkrishnan and John Reif
[8.] The Tile Complexity of Linear Assemblies, ICALP09, with Nikhil Gopalkrishnan and John Reif
[9.] DNA Based Evolutionary Approach for Microprocessor Design Automation, ICANNGA07, with Arjun Kumeresh and Venkateswaran Nagarajan

Conference Posters

[10.] Speeding up DNA Circuits using Localized Hybridization, FNANO11, with Nikhil Gopalkrishnan, Sudhanshu Garg and John Reif
[11.] Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions, FNANO 10, with Nikhil Gopalkrishnan, Bernard Yurke and John Reif
[12.] Design for Experimental Demonstration of Linear Activatable Assemblies, DNA16, with Nikhil Gopalkrishnan, Thom LaBean and John Reif
[13.] A Dendritic Nanostructure for DNA Detection, FNANO09, with Thom LaBean, John Reif, Erik Schultes, Geetha Shetty and Peng Yin
[14.] Structural Optimization of Dendritic DNA Self-Assembly, FNANO09, with Morgan Bishop, John Reif, Thomas Renz, Eric Schultes and Clare Thiem
[15.] Target DNA Detection by Strand Displacement and Deoxyribozymogen Amplification, FNANO09, with Thom LaBean, John Reif, Erik Schultes, Geetha Shetty and Hao Yan
[16.] MMINi-DASS - Large-scale Brain Circuit Construction and Simulation for Interconnectivity Prediction, Neuroinformatics 08, with Vijay Daniel, Vignesh Jaganathan, Ashutosh Mohan, Venkateswaran Nagarajan, Vijay R and Karthik Srinivasan
[17.] Microprocessor Design Automation: A DNA Based Evolutionary Approach, BICS06, with Arjun Kumeresh, Venkateswaran Nagarajan, Vasanth Pachai Perumal and Deephan Venkatesh

Workshop Papers

[18.] DNA Origami: Folding DNA into Desired Shapes, Dhi Yantra09

Selected Project Reports

[19.] Reducing the Effects of Branch Misprediction through Dynamic Heterogeneous Core Scheduling, with Justin Manweiler
[20.] Geometric Duality and Linear Programming, with Sharath Raghavendra
[21.] Biomolecular Detection using DNA Based Nanoparticle Arrays, with Horacio Carias, Staci Vanlue and Viresh Thusu
[22.] Circuit Constructing Turing Machines