John H. Reif

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John H. Reif

My Advise on The Art of Research

Favorite Quotes on Creative Research:

- “Water comes gushing forth from the sand, the deeper and deeper it is dug; likewise, intelligence will grow, the more and more a person studies.” - Thirukkural

- “I have learnt this at least by my experiment, that if one advances confidently in the direction of his dreams in the night, and endeavors to live the life he has imagined, he will meet with a success unexpected in common hours.” –Thoreau

My Books

- Synthesis of Parallel Algorithms, (edited by J. Reif), published by Morgan Kaufmann, Spring, 1993.

- Parallel Algorithm Derivation and Program Transformation, (edited by R. Paige, J. Reif and R. Wachter), published by Kluwer Academic Publishers, June, 1993.

- Handbook of Randomized Computing (Edited by S. Rajasekaran, P. M. Pardalos, J.H. Reif and J. Rolim), published by Kluwer Volume I and II, Academic Press, London, 2001.

- Handbook of Parallel Computing: Models, Algorithms and Applications (Edited by Sanguthevar Rajasekaran and John H Reif), published by Taylor & Francis, Boca Raton, FL. ISBN 978-1584886235 (December, 2007).

- DNA-based Self-assembly and Nanorobotics (by Sudheer Sahu and John H. Reif), VDM Verlag, DNA-Based Self-Assembly and Nanorobotics, Published by VDM Verlag Dr. Mueller e.K., Saarbrücken, Germany, 128 pages, (November 10, 2008).

My Research Publications: most available for download in PDF format

- My publications organized by research area (journal & conf. combined)

- My publications chronographically ordered (journal & conf. combined)

- My publications listed on Duke Faculty Website (journal & conf. separate)

- Lists (but no downloads) of my conference papers are also available from the STOC conference database and the FOCS conference database

My Papers Categorized by Topics (282 downloadable papers)

- Biomolecular Computing and Self Assembly of DNA Nanostructures (99 papers)

- Motion Planning and Kinodynamics in Robotics (30 papers)

- Sequential and Parallel Algebraic and Numerical Algorithms (28 papers)

- Sequential and Parallel Graph Algorithms (24 papers)

- Sequential and Parallel Program Optimization (16 papers)

- Randomized Parallel Algorithms (6 papers)

- Optics and Optical Computing (12 papers)

- Computational Geometry (6 papers)

- N-Body and Molecular Simulations (6 papers)

- Quantum Computing (4 papers)

- Parallel Architectures (6 papers)

- Sequential and Parallel Optimization (3 papers)

- Sequential and Parallel Sorting (5 papers)

- Parallel Parsing (1 paper)

- Distributed and Real Time Algorithms (5 papers)

- Reliable Computing and Fault Testing (5 papers)

- Data Compression Algorithms (11 papers)

- Searching Algorithms and Learning Theory (6 papers)

- Program Logics (6 papers)

- Complexity of Games (5 papers)

- Finance and Investment Theory (2 papers)

- Solar Energy (2 papers)

- Virtual Reality (2 papers)

My Research in Biomolecular Computing and Self Assembly of DNA Nanostructures:

· My Papers in Biomolecular Computing and Self Assembly of DNA Nanostructures

Recent New Releases and Interviews

Faster DNA Computing - Duke Research News (2018)

Invasion Of The Molecular Math Robots - SciWorks NPR Radio(Oct, 2016)

Analog DNA Circuit Does Math In A Test Tube - Duke Today (Aug, 2016)

Download: My Papers in Biomolecular Computing and Self Assembly of DNA Nanostructures

· Book on DNA Computation:

· Sudheer Sahu and John H. Reif, DNA-based Self-assembly and Nanorobotics, VDM Verlag, DNA-Based Self-Assembly and Nanorobotics, Published by VDM Verlag Dr. Mueller e.K., Saarbrücken, Germany, 128 pages, (November 10, 2008) ISBN-10: 363909770X, ISBN-13: 978-3639097702.

· Research Talk Presentations:

Presentations on DNA Computation, Self-Assembled DNA Nanostructures & DNA Robotics:

My Recent Research in DNA Computation:
- Recent Research in DNA Computing [pptx] [pdf]

On DNA Nanodevices:

- DNA-Based Programmable Molecular Devices [pptx] [pdf]

My Research DNA Nanostructures:

- Self-Assembled DNA Nanostructures [ppt] [pdf]

· Some of My Experimental Papers on demonstrations of DNA Nanostructures

Experimental Demonstrations of molecular computation:

· First Experimental Demonstration of molecular computation via Self-Assembly:

Chengde Mao, Thomas H. LaBean, John H. Reif, Nadrian C. Seeman, Logical Computation Using Algorithmic Self-Assembly of DNA Triple-Crossover Molecules, Nature, vol. 407, pp. 493-495 (Sept. 28 2000); C. Erratum: Nature 408, 750-750 (2000).

· Recent Experimental Demonstrations of molecular computation:

Tianqi Song, Abeer Eshra, Shalin Shah, Hieu Bui, Daniel Fu, Ming Yang, Reem Mokhtar, and John Reif, Fast and Compact DNA Logic Circuits Based on Single-Stranded Gates Using Strand-Displacing Polymerase, Nature Nanotechnology (Sept 2019). DOI: 10.1038/s41565-019-0544-5

· Recent Experimental Demonstrations of molecular computation on Cancer Cell Membranes:

Tianqi Song, Shalin Shah, Hieu Bui, Sudhanshu Garg, Abeer Eshra, Ming Yang, and John Reif, Programming DNA-Based Biomolecular Reaction Networks on Cancer Cell Membranes, Journal of the American Chemical Society (JACS), Vol. 141, No. 42, pp. 16539-16543. (Oct 2019). https://doi.org/10.1021/jacs.9b05598 Publicity: https://today.duke.edu/2019/11/id-verification-now-cancer

Experimental Demonstrations of Autonomous Molecular Robots:

· First Experimental Demonstration of Autonomous Molecular Robot:

Peng Yin, Hao Yan, Xiaoju G. Daniel, Andrew J. Turberfield, John H. Reif, A Unidirectional DNA Walker Moving Autonomously Along a Linear Track, Angewandte Chemie [International Edition], Volume 43, Number 37, Sept. 20, 2004, pp. 4906-4911. [PDF] or [PDF] Supplemental Information: [PDF] Abstract: [PDF] Talk: [PDF] [PPT]

· Experimental demonstration of Autonomous Molecular Robot:

Experimental Demonstrations of programmed molecular assembly:

· Peng Yin, Rizal F. Hariadi, Sudheer Sahu, Harry M.T.Choi, Sung Ha Park, Thomas H. LaBean, John H. Reif, Programming DNA Tube Circumferences, Science, Vol. 321. no. 5890, pp. 824–826 (August 8, 2008). [PDF] Supplemental Info: [PDF]

· First Experimental demonstration of programmed molecular patterning:

Hao Yan, Thomas H. LaBean, Liping Feng, and John H. Reif, Directed Nucleation Assembly of Barcode Patterned DNA Lattices, Proceedings of the National Academy of Science(PNAS), Volume 100, No. 14, pp. 8103-8108, July 8, (2003). [PDF] (Publicity)

Experimental Demonstrations of Optical Multiplexing with Temporal DNA Barcodes:

· Shah, Shalin, Abhishek Dubey, and John Reif. "Improved optical multiplexing with temporal DNA barcodes." ACS Synthetic Biology 8.5 (2019): 1100-1111.

- Book on DNA Computation:

My Research in Other Alternative Models of Computation:

- Quantum Computing

- Optical Computing

Overview of My Research in Algorithms:

- Parallel Algorithms for Graphs, Algebra, Geometry and Sorting

- Randomized

- Algebraic and Numerical

- Data Compression Algorithms

Please let me know if you have any problems with these web pages.