CURRICULUM VITAE
John H. Reif
Personal
John Henry Reif
Born: 1951
Madison, Wisconsin
U.S. Citizen
Current Position
Hollis Edens
Distinguished Professor, Trinity College of Arts and Sciences, Duke
University since 2003.
Professor of Computer
Science at Duke University, since 1986.
Secondary appointment in
Department of Electrical and Computer Engineering, Pratt School of Engineering,
Duke University since June, 2016.
Academic
Address Home
Address
D223 LSRC
Building 3112
Devon Road
Dept. of Computer
Science Durham,
NC 27707
Duke University
Box 90129
Durham, NC 27708-0129
U.S.A.
Email address:
Reif DNA Nanoscience
Lab: Room 3245, French Family Science Center
Homepage: https://www.cs.duke.edu/~reif
Research Interests - DNA
nanostructures, Molecular Computation, Efficient Algorithms, Parallel
Computation, Robotic Motion Planning, and Optical Computing.
Recreational Interests -
skiing and cross-country skiing, wind surfing, canoeing and hiking
Education
Ph.D. in Applied
Mathematics (Division of Applied Sciences, Harvard University, Cambridge,
MA, July 1977) Thesis title: Combinatorial Aspects of Symbolic Program
Optimization. Thesis advisor: Harry R.
Lewis (Previously Dean of Harvard College)
M.S. in Applied Mathematics
(Division of Applied Sciences, Harvard University, Cambridge, MA, Spring 1975)
B.S., magna cum laude, in
Applied Mathematics and Computer Science, (Tufts University, Medford, MA,
Spring 1973)
Enrolled in independent
study in mathematics, computation and optics during Fall 1970 - Spring 1973,
funded by a grant from the Sloan Foundation's Unified Science Study Program.
Note: While an
undergraduate Fall 1970 - Spring 1973 at Tufts U., Reif was in the Unified
Science Study Program(USSP), an interdisciplinary independent study program
(spanning mathematics, computer science, physics, and engineering disciplines)
funded by a grant from the Sloan Foundation. His undergraduate projects were
funding under this program and included: stochastic analysis and computer
simulations of neural nets, design of computer made holograms, software for
structural analysis of geodesic domes, and a computer generated a short
animated movie. Reif was given a full scholarship and graduated from Tufts in 3
Years, Magna cum laude.
Wellesley High School,
Wellesley, MA, Spring 1970
Faculty Positions
A. Hollis
Edens Distinguished Professor of Computer Science in Trinity College
of Arts and Sciences, Duke University, September 1, 2003 to
present.
Professor, Duke University,
Summer 1986 to present
Distinguished Adjunct
Professor, Faculty of Computing and Information Technology (FCIT), King
Abdulaziz University (KAU), Jeddah, Saudi Arabia (10/2011-9/2014).
Visiting Professor
(Sabbatical), Carnegie Mellon University, Spring 1994.
Visiting Scientist,
Mathematical Sciences Research Institute, Berkeley, CA, Spring 1986
Associate Professor,
Harvard University, Spring 1983 to Spring 1986
Visiting Scientist
(Sabbatical), Laboratory for Computer Science at M.I.T., Fall 1984
Assistant Professor,
Harvard University, Fall 1979 to Spring 1983
Assistant Professor,
University of Rochester, New York, Fall 1978 to Spring 1979
Research Associate,
University of Rochester, New York, Fall 1977 to Fall 1978
(Research Assistant,
Harvard University, Spring 1975 to Spring 1977)
Memberships, Awards and
Prizes
Awarded: Tufts
Notable, Tufts University, 2010.
Fellow: Association for the
Advancement of Science (AAAS), since 2003.
Fellow: Association for
Computing Machinery (ACM), since 1997.
Fellow: Institute of
Electrical and Electronics Engineers (IEEE) since 1993.
Fellow: Institute of Combinatorics
and its Applications, since 1991.
Awarded: Rozenberg Tulip Award in DNA Computing (Tulip Prize) International
Society for Nanoscale Science, Computation and Engineering (ISNSCE), 2005
Awarded: Harvard University
Thomas Hoopes Prize for directing the undergraduate honors thesis, by Philip N.
Klein (now Full Professor, Brown University), June 1984.
Member: Faculty of 1000, since
2005
Member: International
Society for Nanoscale Science, Computation and Engineering (ISNSCE) Chair
of Scientific Advisory Committee of ISNSCE since 2004.
Member: Society of
Industrial and Applied Mathematicians (SIAM)
Member: American
Mathematics Society (AMS)
Member: Sigma Xi Scientific
Research Society
Listed: ISI
(Thomson Reuters) Highly Cited Researcher,
Computer Science
Listed: Who's Who in
America, Who's Who in the World, Who's Who in Emerging Leaders in America,
Who's Who in Science and Engineering, Who's Who in American Education.
Current Postdoc Supervision
Daniel
(Dan) Fu, Research topic: “DNA Computation on Cell Membranes” and
“Casting Metallic Nanoparticles in Multi-layered Encapsulating 3D DNA
Nanostructure”. Jan. 2022-current.
Xin Song,
Research topic: “DNA computation and COVID-19 detection RT-LAMP
protocols”, 2021-current.
Prior Postdoc Supervision
Xiaoju Guan (jointly
supervised with Hao Yan), 2003-2005 (now Inner
Mongolia Medical University, China).
Sang Jung Ahn (jointly
supervised with Thom LaBean), 2003-2004. (Later postdoctoral fellow at the California Institute of Technology. Currently
Research Scientist, Korea Research Institute of Standards and Science, Daejeon,
South Korea)
Dage Liu, Postdoc 2001-2004 (Later Research Associate at North
Carolina State University, University of Wisconsin-Madison , and Univ. of Penn.)
Hao Yan, Postdoc 2001-2002 and Research Assistant Professor, CS Dept,
Duke University, 2002-2004 (Currently Distinguished Professor, Chemistry
and Biochemistry Department, Arizona State University, August 2004-current.)
Thom
LaBean, Postdoc 1998-2001 (Associate Professor, Materials Science &
Engineering, North Carolina State University. Previously Research
Associate Professor, CS Dept, Duke University)
Sandeep
K. S. Gupta, Postdoc 1995 (currently Professor, Department of
Computer Science and Engineering, Ira A. Fulton School of Engineering, Arizona
State University, Tempe, AZ 85287-5406).
Lars
Nyland, Postdoc 1991-1991 (Currently Senior Architect, NVIDIA,
Durham, NC and Adjunct Associate Professor, Department of Computer
Science, University of North Carolina, Chapel Hill, NC.)
Steven
Tate, Postdoc 1991-1993 (Currently Professor and Chairman, Department
of Computer Science, University of North Carolina at Greensboro,
Greensboro, NC)
Hillel
Gazit, Postdoc 1989-1991 (Currently Software Consultant, San
Francisco, CA)
Paul G.
Spirakis, Postdoc 1982-1982 (Currently Full Professor and Chairman,
Department of Computer Science, University of Liverpool, UK and Professor,
Department of Computer Engineering & Informatics, University of Patras,
School of Engineering, Patras, Greece and Director Computer Technology
Institute, Patris, Greece.)
Current Graduate Students
(Ph.D. candidates)
Rajiv Nagipogu,
Tentative Ph.D. thesis topic: “Adaptive molecular computing systems”. Projected
Date of Graduation: Fall 2025.
Graduate Student Supervision (Completed Degrees):
Dan Fu:
Ph.D. thesis topic: “Design Optimization of Encapsulating 3D DNA
Nanostructures with Curvature and Multi-layers”. Date of Graduation: Dec. 2022.
Xin Song: Ph.D. thesis
topic: “Novel Techniques and Applications in
Molecular Computing, Data Storage, Diagnostics, and Fabrication”. Date of Graduation: Fall
2021.
Ming Yang: M.S,
thesis topic: “Social DNA Nanorobots”. Graduation: Fall
2021.
Shalin
Shah, Ph.D. thesis: “Programming DNA for Molecular-Scale
Temporal Barcoding and Enzymatic Computation”. Date of Graduation: Spring 2020.
Abeer Eshra: Ph.D.
thesis: “Computing Machine Implementation using DNA - Reusable DNA Circuits”.
Menoufia University Department of Computer Science and Engineering. Date of
Graduation: Spring 2019. (Currently Postdoc with Damian Woods at at Maynooth
University, Ireland)
Reem
Mokhtar, M.S. thesis: “Modeling DNA Nanodevices
Using Graph Rewrite Systems”. Date of Graduation: Spring 2019.
Tianqi
Song, Ph.D. thesis topic: “Theory and
Experiments in DNA Analog Computation”. Date of Graduation: Summer 2018.
(Currently Postdoc at Cal Tech).
Hieu Bui, Ph.D. thesis
topic: “Localized DNA Computation”. Date of Graduation: Spring
2017. (Currently National Research
Council Postdoctoral Research Fellowship at the U.S. Naval Research Laboratory (NRL)).
Sudhanshu
Garg, Ph.D. thesis topic: “Programming Molecular Devices using
Nucleic Acid Hairpins
”. Date of Graduation: May 2016. (Currently Research
Scientist at LinkedIn, Sunnyvale, California).
Nikhil
Gopalkrishnan, Duke
University Ph.D. thesis topic: “Computational and Experimental DNA
Self-Assembly”. Date of Graduation: Fall 2012. (Currently Postdoctoral
Assistant, Department of Systems Biology, Harvard
Medical School, Cambridge, MA in the laboratory of Peng Yin. Now Director of
Research at 3EO Health, Inc.)
Harish Chandran, Duke
University Ph.D. thesis topic: “A Theoretical and Experimental Study of
DNA Self-assembly”. Date of Graduation: Fall 2012. Currently Research
Scientist, DeepMind, Mountain View, California 94043 (Previously
2012-2017, Research Scientist and Tech
Lead Manager at Google Research, Google Corporation, Redwood
Shores, California.)
Tianqi
Song, Duke University Masters thesis topic:
“Stochastic DNA Tiling Assembly”. Date of Masters Graduation: Spring
2012.
Ahsan
Muhammad, Duke University Masters thesis topic: “Cluster
Quantum Computing”. Date of Masters Degree Graduation: Spring 2012.
Samuel Slee, Duke
University Ph.D. thesis: “Developing Scalable Abilities for
Self-Reconfigurable Robots”. Dec. 1, 2010. (Currently Research
Scientist at Google Research, Google
Corporation, Redwood Shores, California.)
Urmi
Majumder (also co-advised by Thomas LaBean), Duke
University Ph.D. thesis: “Molecular Computing with DNA Self-Assembly”.
March 30, 2009. [PPT] [PDF]
(Currently Senior Software Developer/Architect at Oracle
Corporation, Washington D.C)).
Sudheer
Sahu, Duke University Ph.D. thesis: “DNA based self-assembly
and nanorobotics: Theory and Experiments”, December, 2007 [PDF] Slides: [PPT] [PDF]. (Previously
Research Scientist, Microsoft Live Search, in
Redmond, Washington. Currently Executive
Director of Engineering: Data, Search, and Application Services,
Microsoft, Los Angeles Area, Microsoft.)
Peng Yin, Duke
University Ph.d thesis: Theoretical and Practical Study in DNA Based
Self-Assembly, Nanorobotics, and Nanocomputation. May, 2005 [PDF] [abstract] Slides:
[PPT] [PDF].
(2005-2009, CPI Postdoctoral Researcher, Caltech, Pasadena, CA).
(Currently Full Professor, Department of Systems Biology, Harvard Medical
School, Cambridge, MA. Also Founder, 3EO Health, Inc.)
Sung Ha
Park, Duke University Ph.D. thesis: “Self-assembled DNA
Nanostructures and DNA-templated Silver Nanowires” Thesis: [PDF] Slides:
[PPT] [PDF] (Reif
was secondary adviser only; primary supervisors are Thom LaBean and Gleb
Finkelstein (Dept of Physics), Department of Physics, May, 2005
(2005-2007, CPI
Postdoctoral Researcher, Caltech, Pasadena, CA), (Currently
Associate Professor, Sungkyunkwan University, South
Korea).
Zhung (Robert)
Sun, Duke University Duke University Ph.D. thesis: Complexity of
Robotic Movement Problems. Date of Graduation: April 2003 [PDF] [abstract] Slides:
[PPT] [PDF]. Masters
Thesis "The Computational Power of Frictional Mechanical Systems, May,
1999. (Currently Assistant Professor Hong Kong Baptist University ,
Former: Research Scientist, Google
Inc., Mountain View, CA)
Guo Bo, Duke University
Master Thesis "Computing by DNA Self-Assembly". Oct, 2001 (currently
Research Scientist, Mitsubishi Electric, Japan).
Yuan Guangwei, Duke
University Master Thesis "Simulation of DNA Self-Assembly", Fall 2000
(Currently Research Scientist, China).
Christopher Butler, Duke
University Master Thesis "Simulations of Molectronics architectures",
2000.
Xavier Berni: Duke
University MS Thesis "DNA tagging", May 2000. (Currently
Computer Scientist Consultant, S. Carolina)
Deganit
Armon, Duke University Ph.D. Thesis "Dynamic Data
Structures for Randomized Algorithms that use Sampling", 1997.
Thesis: [PDF] [abstract] Lecturer
at Afeka Tel Aviv Academic College of Engineering.
Ashish
Gehani, Duke University Masters Thesis "Image Resolution
Enhancement via Data Compression Techniques", 1997 (Currently Senior
Computer Sciencist, SRI International, Menlo Park, CA. Previously Research
Assistant Professor, Department of Computer Science and Engineering, University
of Notre Dame.)
Shenfeng
Chen, Duke University Ph.D. Thesis "Algorithmic
Applications of Data Compression Techniques", 1996. Thesis: [PDF] [abstract]. Currently
Technical Manager of a startup company in China.
Hongyan Wang, Duke
University Ph.D. Thesis “Approximate and Adaptive Algorithms for Some
Optimal Motion-Planning Problems,” 1996 Thesis: [PDF] [abstract] (Currently Adjunct
Faculty member of University of Maryland University College. Previously
senior software engineer with Parametric Technology Corporation in
Massachusetts and with Canopus, Ltd. in Kobe, Japan.).
Zhiyong Li, Duke
University Ph.D. Thesis "Computational Models and Program Synthesis
for Parallel Out-of-Core Computation", May, 1996 [PDF] [abstract]. (Currently
Research Scientist, Sun Microsystems, California)
Akitoshi
Yoshida, Duke University Ph.D. Thesis "Applications of
Optical Techniques in Interconnections, Image/Video Compression, and
Computational Geometry", 1994, Univ. Microfilms Int. 9424616 [abstract] (Currently
Research Scientist, Computing Center of the University of Mannheim, Germany).
Salman Azhar (J.P.
Duke Fellow as Graduate Student), Duke University Ph.D. Thesis
"Computational Aspects of Multiagent Systems: Modeling Efficiency and
Computing Sequential Equilibrium", 1993, Univ. Microfilms Int. 9420402 [abstract].
Masters Thesis "Efficient Learning of Permutation Groups by
Examples", 1990 (Currently Visiting Professor of the Practice,
Dept of Computer Science, Duke University. Previously Executive Consultant at
Eike Consulting, LLC and Advisor (2008-2014) & VP Engineering (2006-08) at
DecisionStreet, Inc. Previously Associate Professor at University of San
Francisco.)
Peter Su, Dartmouth
University Ph.D. Thesis (Ph.D. completed at Duke but Scott Drysdale was
official Supervisor) "Efficient Parallel Algorithms for Closest Point
Problems", 1994 Univ. Microfilms Int. 9524419 (Previously
Research Assistant Professor, Software Institute, Carnegie Mellon University.)
Tassos
Markas, Duke University Ph.D. Thesis "Data Compression:
Algorithms and Architectures", 1993, Univ. Microfilms Int.
9405986 [abstract]. (Currently
President & CEO, 3DMedia, RTP, NC. Previously Director of Multimedia, Atmel
Corporation, San Jose, CA. Previously Research Scientist, VLSI Design and Test
Department, Center for Digital Systems Engineering, Research Triangle Institute,
RTP, NC.)
Steven
Tate, Duke University Ph.D. Thesis "Arithmetic Circuit
Complexity and Motion Planning", 1991, Univ. Microfilms Int.
9127527 [abstract]. (Currently
Professor and Chairman, Department of Computer Science, University of
North Carolina at Greensboro, Greensboro, NC.)
Lars
Nyland, Duke University Ph.D. Thesis "The Design of a
Prototyping Programming Language for Parallel and Sequential Algorithms",
1991, Univ. Microfilms Int. 9127499 [abstract]. (Currently Senior
Architect, NVIDIA, Durham, NC and Adjunct Associate Professor,
Department of Computer Science, University of North Carolina, Chapel Hill, NC.)
Sandeep
Sen, Duke University Ph.D. Thesis "Random Sampling
Techniques for Efficient Parallel Algorithms in Computational Geometry",
1989, Univ. Microfilms Int. 9025050 [PDF] [abstract] (Currently
Full Professor, Department of Computer Science & Engineering, Indian
Institute of Technology, Delhi, India).
Sanguthevar
Rajasekaran, Harvard University Ph.D. Thesis "Randomized Parallel
Computation", 1988, Univ. Microfilms Int. 8909005. (Currently
UTC Chair Professor of CSE and Director of the Booth Engineering Center for
Advanced Technologies (BECAT), Computer Science and Engineering Department,
University of Connecticut.)
Paul G.
Spirakis, Harvard University Ph.D. Thesis "Probabilistic
Algorithms", Dec. 1981, University Microfilms International No. 8216206.
(Currently Professor and Chairman, University of Liverpool, UK and
Professor, Department of Computer Engineering & Informatics, University of
Patras, School of Engineering, Patras, Greece and Director Computer Technology
Institute, Patris, Greece.)
Undergraduate Thesis
Supervision
Philip
Klein; Harvard University Undergraduate Thesis(awarded Thomas T. Hoopes
prize) "Stacktracking: Parallel Acceptance of Deterministic Context-Free
Languages", 1984 (Currently Full Professor, Brown University).
Research Support: Principal
Investigator or Co-Investigator
NSF CCF-2113941, SHF:
Small: High-speed DNA polymerase CRNs for signal amplification, oscillation,
consensus, and linear control (PI John H. Reif), 10/01/2021-03/31/2023,
$499,951.
NSF CCF-1909848, SHF:
Small: Distributed DNA Computations Operating on a Collection of Cell Membranes
Polymerase (PI John H. Reif), 10/01/2019-09/30/2022, $300,000.
NSF CCF-1813805, SHF:
Small: Hot DNA Computation: Speeding up DNA-based Computation using
Strand-Displacing Polymerase (PI John H. Reif), 10/01/2018-09/30/2021,
$200,000.
NSF CCF-1617791, SHF:
Small: DNA Circuits for Analog Computations, 6/30/2016 - 6/30/2019, $308,001.
NSF CCF-1320360, SHF:
Small: Localized DNA Hybridization Computation (PI John H. Reif), 8/6/2013
– 7/30/2016, $400,000.
NSF
CCF- 1217457, SHF: Small: Error Correction for Biomolecular
Computations (PI John H. Reif), 7/1/2012 – 6/30/2015, $449,998.
NSF CCF-1141847, EAGER:
Exploratory Software Development & Experiments of Dynamic DNA
Nanosystems (PI John H. Reif), 9/1/2011 – 8/31/2013, $199,997.
NSF
EMT Grant CCF-0829797: EMT/NANO: Autonomous Programmable DNA Devices
Using DNAzymes (PI John H. Reif), 09/4/2008-08/31/2011, $200,000.00.
NSF
EMT Grant CCF-0829798: EMT/NANO: Polymerase-Based Self-Activating and
Reactivating DNA Systems, (PI John H. Reif with coPI Thomas H.
LaBean), 09/01/2008-08/31/2009, $200,000, with expected continued support
for 2009 and 2010 for $150,000/year.
AFSOR
Contract FA9550-08-1-0188, Bio-X-AFSOR: Encapsulated DNA-Based
Molecular Autonomous Sensing Devices With Photonic Output (PI John H.
Reif), April, 2008-Dec 2008, $200,000
NSF
EMT Grant CCF-0551965: EMT: NSF Workshop: Emerging Opportunities
of Nanoscience to Energy Conversion and Storage (PI John H. Reif),
September 1, 2005- September 1, 2006,
$49,900. https://www.cs.duke.edu/~reif/NSF.NanoEnergy/
NSF
EMT Grant CCF-0523555: EMT: A DNA-Based Autonomous Programmable
Molecular Transport Network (PI John H. Reif with coPI Thomas H. LaBean),
July 15, 2005- August 31, 2007, $300,000
NSF
EMT Grant CCF-0523558: EMT: NSF Workshop of Programmed
Self-Assembly (PI John H. Reif), May. 1, 2005-October 31, 2005, $30,000.
NSF
EMT Grant CCF-0432038: Nano: Error-Resilient DNA Tiling
Assemblies (PI John H. Reif with coPI Thomas H. LaBean), Sept. 1,
2004-Aug. 30, 2007, $295,000.
NSF EMT Grant CCF-0432047:
NANO: Combinatorial Self-assembly of Nanocircuits on Addressable DNA
Nanoscaffolds (PI Hao Yan with coPIs: Chris L. Dwyer, Gleb Finkelstein, John H.
Reif, Thomas LaBean), Sept. 1, 2004-Aug. 30, 2007, $300,000
Taiko Denki
Inc. Industrial Grant: Applications of DNA Self-Assembly Nanofabrication
Technology to Molecular Scale Electrical Contacts (PI John H.
Reif with coPI Thomas H. LaBean), Taiko Denki Inc., Tokyo, Japan,
Jan. 1, 2004-Dec. 30, 2005, $110,000.
NSF ITR 0326157:
Nanoarchitecture: Balancing Regularity, Complexity and Defect Tolerance using
DNA for Nanoelectronic Integration(PI: Alvin LeBeck CoPIs: Dan Sorin, Jie Liu,
John H. Reif, Thom LaBean, Hao Yan, Sean Washburn, Dorothy Erie, Paul Franzon),
Sept 1, 2003- Aug 31, 2006. $1,200,000.
NSF QuBIC
EIA-0218376: Novel DNA Nanostructures for Targeted Molecular Scale to Micro
Scale Interconnects. (PI: Thomas H. LaBean, CoPI: John H. Reif) NSF EIA-0218376, Sept 1, 2002- Aug 31, 2005. $349,999.
NSF EIA-0218359:
Molecular Robotics for DNA Nanostructures. (PI: Hao Yan, CoPI: John H. Reif),
Sept 1, 2002- Aug 31, 2005. $349,995.
Taiko
Denki Inc. Industrial Grant: DNA Self-Assembly
Nanofabrication Technology to Molecular Scale Electrical Contacts (PI John
H. Reif with coPI Thomas H. LaBean), Taiko Denki Inc., Tokyo, Japan,
Sept. 1, 2002- Sept. 30, 2003, $60,000.
Programmable DNA Lattices:
Design, Synthesis and Applications (PI John H. Reif), BioComp Program, DARPA/AFSOR Contract, F30602-01-2-0561 July
1, 2000-Dec 30, 2004, $2,550,000.
Supplemental Augmentation to: Programmable DNA
Lattices: Design, Synthesis and Applications (PI
John H. Reif), BioComp Program, DARPA/AFSOR Contract, F30602-01-2-0561 Jan 1, 2002-Dec 30, 2002, $112,662 for FY2002.
Micro and Nano-Robotics
Motion Control Algorithms (PI John H. Reif), NSF SEGR Award
NSF-11S-01-94604, Sept 1, 2000-Sept 30, 2001, $80,772.
NSF ITR Grant EIA-0086015: Supplemental Augmentation to: Self-Assembly
of DNA Nano-Scale Structures for Computation (PI John H. Reif), additional
$413,000 awarded in FY 2004.
NSF ITR
Grant EIA-0086015: Self-Assembly of DNA Nano-Scale Structures for
Computation, (PI John H. Reif), Sept 1, 2000-Sept 30, 2005, $2,019,999.
(awarded $1,184,999 September
1, 2000-August 31, 2003.
Prototyping
Biomolecular Computations, (PI John H. Reif), jointly funded by Defense
Advanced Research Projects Agency and National Science Foundation, NSF CCR-9725021, July 1997-Sept 2001, $2,748,017.
Moleware
and the Molecular Computer, Subcontract PI (overall PI: James M.
Tour), DARPA/ONR N00014-99-1-0406, 01 Mar 99
through 28 Feb. 2001, Subcontract $50,000.
Robust, Adaptive and Dynamic Robotic Motion Planning, (PI John
H. Reif), NSF Grant NSF-IRI-9619647,
5/97-06/2000, $295,000.
SEGR: Design of a
Biomolecular Distributed Operating System, (PI John H. Reif), NSF Grant CCR-9810000,
Aug 1998-1999, $50,000.
CURIOUS: (C)enter for
(U)ndergraduate Education and (R)esearch: (I)ntegration Thr(OU)gh
Vi(S)ualization, (Co-principal investigator). NSF CDA-96-34475 09/96 - 08/99 $
405,200
Acquisition of a
Workstation Cluster Testbed for Next-Generation Collaborative Computing
(Co-principal investigator). National Science Foundation Grant contract
CDA-95-12356, 09/95 - 08/98, $489,600
Multidisciplinary Research
for Demining, (Co-principal investigator of subcontract with E. Gelenbe, N
Schmajuk and J. Staddon,) Army Research Office(ARO) contract DAAH-04-96-1-0448,
11/96 - 10/99, total contract: $3,000,600, Subcontract $431,000./year.
An Exploratory Study of
Parallel Molecular Computation, (PI John H. Reif) National Science Foundation
Grant number CCR-96-33567, 08/96 - 07/97 $50,000
Toward Autonomous Robots:
Robust, Adaptive and Dynamic Motion Planning, (PI John H. Reif), National
Science Foundation Grant NSF-IRI-91-00681,02/92 - 01/97, $365,755,
SIMD/MIMD Parallel
Computing: Computational Theory, Scientific Applications, and Systems Research,
(Co-principal investigator with C.S. Ellis, C. Gardner, H.S. Greenside, D.W.
Loveland, and D.J. Rose) National Science Foundation Grant number CDA-91-23483,
CISE Institutional Infrastructure Program, 09/92 - 08/98, $1,420,001 plus
institutional support of $421,209.
A Refinement-Based
Methodology for the Architecture-Independent Design and Development of Parallel
Software, (Co-principal investigator with Andrew Goldberg and Jan Prins). Rome
Laboratory contract F30602-94-C-0037, Subcontract to Kestrel Development Corporation,
$314,495.
Common Prototyping Language
(CPL) based on SETL, REFINE, and UNITY, DARPA/ISTO contract N00014-92-C-0182
under subcontract KI-92-01-0182 from Kestrel Institute, Additional $665,147,
September 1, 1992 through August 31, 1995
Common Prototyping Language
(CPL) based on SETL, REFINE, and UNITY, DARPA/ISTO, Subcontracted from Kestrel
Institute, Additional $240,000, May 1, 1991-March 30, 1992.
Derivation and Analysis
Tools for the Synthesis and Implementation of Parallel Algorithms, (PI John H.
Reif), DARPA/ISTO contract N00014-91-J-1985, $1,560,000, July 1, 1991-June 30,
1994.
Parallel Compression of
Space and Earth Data, (PI John H. Reif), NASA, Prime Contract Number:
NAS5-30428, Subcontract 550-63, $491,699, October 1, 1991-September 30,
1993.
Randomized Methods in
Distributed and Parallel Computation, (with B. Chor), Binational Science
Foundation, $36,000, September 1, 1989-August 31, 1992.
Common Prototyping Language
(CPL) based on SETL, REFINE, and UNITY, DARPA/ISTO, Subcontracted from Kestrel
Institute, $162,240, October 1, 1989-September 30, 1990.
Very High Speed Holographic
Message Routing for Parallel Machines, (PI John H. Reif), DARPA/ARMY, $290,673,
September 1, 1988-August 31, 1990.
Parallel Compression of
Space and Earth Data, (PI John H. Reif), NASA, $435,000, October 1,
1988-September 30, 1991.
Parallel Algorithm
Derivation, (PI John H. Reif), DARPA/ISTO, $696,899, July 1, 1987-June 30,
1991.
Computational Complexity
and Efficiency in Electro-optical Computing Systems, (PI John H. Reif), Air
Force Office of Scientific Research, $442,772, September 1, 1987-August
31,1990.
Randomized Parallel
Algorithms in Learning, (PI John H. Reif), Office of Naval Research, $228,707,
January 1, 1987-February 28, 1989.
Randomized Techniques for
Highly Parallel Computing, (PI John H. Reif), Office for Naval Research,
$93,475, July 1, 1984-June 30, 1986.
Parallel and Probabilistic
Computations, (Co-Investigator with H. R. Lewis) National Science Foundation,
$113,455, July 1, 1982-December 31, 1984.
Distributed
Multi-processing, (PI John H. Reif), Office for Naval Research, $132,000, July
1, 1980 -June 30,1984.
Graph Algorithms in Program
Analysis and Topological Imbeddings, (PI John H. Reif), National Science
Foundation, $25,000, October 1, 1979-July 31, 1982.
Experimental Projects:
Hardware, Software and Biochemistry
1. (Current) President of
Eagle Eye, Inc., a small business based in the Research Triangle, NC. It was
originally engaged in reconnaissance multi-spectral image target recognition.
EagleEye, Inc. now specializes in contract research in the areas of defense
applications of DNA biotechnology. Eagle Eye, Inc. has executed a number of
federal research contracts over the last three years. In 2000, Eagle Eye
developed (in collaboration with M. Pirrung, Dept of Chemistry, Duke Univ.) a
biomolecular system for associative search in pedabit size DNA libraries.
2. DNA Tagging Project(with
C. X. Berni, C. Kingsford) We made improvements to SAGE tagging to allow the
technology to be applied to universal DNA hybridization arrays. Also, developed
simulation software for the improved tagging process with a highly interactive
graphic interface.
3. (Previous) Chief
scientist of Rtware, 1995-1999, which produces real-time control software which
is currently used for both commercial and military applications; military
customers include the Airforce and Navy. RTware has received a Phase I SBIR
from ONR, It was bought out by Datacode (a large hardware corporation) in 1999.
4. (Previous)
President of RSIC Associates, which received a Phase I and Phase II NASA Small
Business Innovation Research Grant to build very high rate (.20 gigabit/second)
lossless data compression hardware system that was successfully demonstrated.
The multiprocessor chip (1.2 micron CMOS with approx. 330,000 transistors and
with 128 specialized systolic processor cells per chip) was been fabricated and
tested. A number of compression boards, each containing 16 of these chips, have
been running since spring, 1992 and can be used by remote login to MCNC. In
collaboration with Professor Jim Storer of Brandeis University. VLSI design by
Research Triangle Institute, Research Triangle Park, NC in 1989. Board Level
Design by MCNC, NC. Also funded by DARPA/ISTO for MOSES fabrication by HP. RSIC
Associates has received contracts totaling $1,200,000 from various defense
agencies, for the development of this hardware.
5. Co-architect
of BLITZEN (with Ed Davis), a 16,000 processor Massively Parallel Machine under
NASA contract at Microelectronics Center of North Carolina (MCNC). The main
component of the system was a BLITZEN chip, consisting of 128 bit serial
processors (.25 gigabits/second). This chip is 1.2 micron CMOS and has
1,100,000 transistors, making it the largest (nonmemory) chip manufactured in
the world during early 1989. The chip is tested and functional. A prototype
BLITZEN system has been running since spring, 1989. See Publications
(references #73,76).
6. Inventor
of Holographic Based Message Routing Systems for Massively Parallel Machines.
The prototype was constructed under DARPA Contract by Kristina Johnson at the
Center for Electro-Optical Computing Systems, Boulder, CO, April 2, 1989. See
Publications (reference #80).
7. Implementation
(in collaboration with Charles Leiserson, Jill Mesirov, Lena Nekluvova, Steven
Omohandro, and Washington Tayler) of Parallel Nested Dissection Algorithms for
Solution of Large Sparse Linear Systems on the 64,000 process Connection
Machine. Thinking Machines, Inc., Cambridge, MA, 1985-1986. See Publications
(reference #62).
8. Implementation
(in collaboration with John Dorband and Torstein Opsahl) of Parallel Nested
Dissection on 16,000 Processor Massively Parallel Processing Machine (MPP),
NASA Goddard Space Center, Greenbelt, MD, 1985-1986. See Publications
(reference #63).
Patents
1. John H
Reif, Peng Yin, Thomas H. LaBean, Geetha Shetty, Erik A. Schultes, Analyte
Detection Using Autocatalytic Chain Reactions, US Non-Provisional Patent
Application 11/775,740, filed July 10, 2007, publication Date: April 2,
2009. [PDF]. Approved,
issued Oct 25, 2011 as US Patent 8,043,810 B2 [GooglePatent][USPO]. Assignee:
Eagle Eye Research, Inc.
2. John H
Reif, Thomas H. LaBean, Erik A. Schultes, Autonomous
in Vitro Evolution, US Non-Provisional Patent
Application 12/042,276, filed July 10, 2007, publication: September 10,
2009 [GooglePatent][USPO]. Assignee:
Eagle Eye Research, Inc.
3. John H
Reif and Katie L. Reif (joint inventors), "Solar
Concentrator System for Solar Energy Plants",
US Non-Provisional Patent Application 12/889,313, filed Sept 23,
2010 [GooglePatent][USPO]. Also,
Australian Patent number 61/245,250, filed Sept 23, 2009, granted July 24,
2014. Assignee: Eagle Eye Research, Inc.
4. John H
Reif and Karl F. Bohringer, “Microelectronic
Devices for Harvesting Vibrational Energy and Associated Systems and Methods”, US
Provisional Patent Application 61/417,362, filed Nov 29, 2010, published
June 7, 2012, US Non-Provisional Patent Application US 12/0139389. Assignee:
Ruamoko MEMS, Inc.
5. John H
Reif, “Levitation with switchable inductive element and associated
systems, devices, and methods”, Provisional Patent Application 61561918,
Filed Nov 20, 2011, US Non-Provisional Patent Application No. 13/682,712 filed
Nov 20, 2012. Approved Dec 24, 2014. Issued as U.S.
Patent No. 9,024,487 on May 5, 2015. Assignee: Eagle Eye Research, Inc. [GooglePatent][USPO].
7. John H
Reif and Xin Song, "Methods and Systems for Photopatterning and
Miniturization. U.S. Provisional Patent Application Serial No. 62/970,311 filed
February 5, 2020. Also, Patent Cooperation Treaty (PCT) International
Application No. PCT/US2021/016830 filed February 5, 2021. US Patent Number
17/797,765 Issued 08/05/2022. Assignee: Duke University
8. John H
Reif and Xin Song, “Molecular test kit for rapid at-home testing of COVID-19
and other infectious diseases”, U.S. Provisional Patent Application No.
63/164,098, filed Mar. 22, 2021. Assignee: Duke University. Licensed to Domus
Diagnostics, Inc.
9. John H
Reif and Xin Song, "Composition and Methods for Rapid COVID-19 Detection”,
Patent Cooperation Treaty (PCT) International Application No.
PCT/US2022/021138, filed Mar. 21, 2022. Assignee: Duke University. Licensed to
Domus Diagnostics, Inc. John H Reif and Xin Song, "Composition and Methods
for Rapid COVID-19 Detection”, Non-Provisional US Patent Application No. 18/551,547,
filed Sept. 30, 2023. Assignee: Duke University. Licensed to Domus Diagnostics,
Inc.
10. John
H Reif and Xin Song, “Universal Lamp Assays for Detection of Nucleic Acid
Targets”, U.S. Provisional Patent Application 63/191,590, filed May 21, 2021. United
States Patent Application 17/749,858 filed May 20, 2022. Also, Patent
Cooperation Treaty (PCT) International Application No. PCT/US2022/030312, filed
May 20, 2022 and published as PCT/US2022/030312. Assignee: Duke University. Licensed
to Domus Diagnostics, Inc.
11. John H Reif and Xin Song, “Cascaded Nucleic Acid Protocols for Ultra-Specific Molecular Detection, Transduction, and Amplification”, Provisional Patent Application 63/315,635 filed Mar. 11, 2022. Assignee: Duke University. Licensed to Domus Diagnostics, Inc. John H Reif and Xin Song, “Cascaded Nucleic Acid Protocols for Ultra-Specific Molecular Detection, Transduction, and Amplification”, Non-Provisional US Patent Application 18/116,138 filed Mar. 1, 2023. Assignee: Duke University. Licensed to Domus Diagnostics, Inc.
12. John H Reif, Jacquelyn M. Walejko and Xin Song, “Methods and Compositions and Methods for Rapid Molecular Diagnostics with Unified-One-Pot Sample Processing, Nucleic Acid Amplification, and Result Readout”, Provisional US Patent Application 63/408,020 filed Sept 19, 2022. Assignee: Duke University. Licensed to Domus Diagnostics, Inc. John H Reif, Jacquelyn M. Walejko and Xin Song, “Methods and Compositions and Methods for Rapid Molecular Diagnostics with Unified-One-Pot Sample Processing, Nucleic Acid Amplification, and Result Readout”, Non-Provisional US Patent Application 18/370,117 filed Sept 19, 2023. Assignee: Duke University. Licensed to Domus Diagnostics, Inc. John H Reif, Jacquelyn M. Walejko and Xin Song, “Methods and Compositions and Methods for Rapid Molecular Diagnostics with Unified-One-Pot Sample Processing, Nucleic Acid Amplification, and Result Readout”, Patent Cooperation Treaty (PCT) International Application No. PCT/US2023/033141 filed Sept 19, 2022. Assignee: Duke University. Licensed to Domus Diagnostics, Inc.
13. John H
Reif, “Ultra-Cool and Thermochromic Roof and Siding Coatings”, Provisional US Patent
63/313,860, filed 2/25/2022. Assignee: Eagle Eye Research, Inc. John H Reif, “Ultra-Cool
and Thermochromic Roof and Siding Coatings”, Patent Cooperation Treaty (PCT)
International Application No. PCT/US2023/062990 filed Feb 24,2023.
Assignee: Eagle Eye Research, Inc.
14. John H Reif and Xin Song, “Methods and Algorithms for Enhancing the Visualization, Classification, and Interpretation of Colorimetric Assay Readouts for Vision-Norman and Vision-Deficient Users”, Provisional US Patent Application 63/522,872, filed June 23, 2023. Assignee: Duke University. Licensed to Domus Diagnostics, Inc.
Consulting Positions
1. NASA
Johnson Space Flight Center, consultant on Consolidated Space Operations
Contract, Houston, Texas, July, 1997.
2. NASA ICASE Space Flight
Center, Norfolk, Virginia, July, 1996.
3. NEC research center,
Princeton New Jersey, July, 1995.
4. RTware,
NC, real time software and algorithms, 1993.
5. Department
of Mathematical Sciences, IBM Watson Research Institute. Yorktown Heights, NY,
Summers of 1983 and 1984.
6. GTE
Laboratories, VLSI Design Project. Waltham, MA, Spring and Summer 1985.
7. Thinking
Machines, Inc. Connection Machine Project. Cambridge, MA, 1985-1988.
8. Barakat
Associates, Air Force contract: Optical Devices and Optical Computing.
Lexington, MA, Fall 1985.
9. MRJ,
Park and Elmer, Design of Parallel Algorithms for the Connection Machine.
Fairfax, VA, 1985-1988
10.NASA Goddard Space
Flight Center, Space Data and Computing Division, Massive Parallel Processing
(MPP) Project. Greenbelt, MD, 1985-1988.
11.Microelectronic Center
for North Carolina (MCNC), 2nd Generation Massively Parallel Processor Project,
(PI of $300,000 NASA contract supporting this work), initiator of and
co-architect (with Ed Davis) of BLITZEN 128 processor chip, 1986-1988. (see System
Projects #2)
Journals and Book Series
Advisory Boards
1. Editor, Special
Issue on STOC2003, (devoted to selected papers from the 34th Annual ACM
Symposium on Theory of Computing (STOC2002), Journal of Computer and System
Sciences (JCSS), Volume 67. No. 2, Sept. 2003, pp. 211-471. [PDF]
2. Member of
Editorial Board of the Journal of Computational and Theoretical Nanoscience
(CTN), American Scientific Publishers, USA, 2004-2006.
3. Member of
Advisory Board, Theory and Practice of Object Systems, Wiley, New York,
2000-2007.
4. Member of
Editorial Board of the Journal of Experimental Nanoscience, Taylor
and Francis, USA, 2006 - current.
Conference Organizations
1. Member
of Program Committee, Aegean Workshop on Computing, Corfu, Greece, June 1986.
2. Member
of Program Committee, 20th Symposium on Theory of Computer Science, May 1988.
3. Member
of Program Committee, 3rd International Conference on Supercomputing, Boston,
Massachusetts, May 1988.
4. Chairman
of Program Committee, Aegean Workshop on Computing, Corfu, Greece, June 1988.
5. Member
of Program Committee, 2nd Symposium on Frontiers of Massively Parallel
Computing, Fairfax, Virginia, October 1988.
6. Member
of Program Committee, 22nd Symposium on Theory of Computer Science, May 1990.
7. Member
of Program Committee, 4th Symposium on Frontiers of Massively Parallel
Computing, Fairfax, Virginia, October 1990.
8. Program
co-Chairman, First IEEE Conference on Data Compression, Snowbird, Utah, April
1991. (Sponsored by IEEE Computer Society)
9. Member
of Program Committee, 32nd IEEE Symposium on Foundations of Computer Science,
October 1991. (Sponsored by IEEE Computer Society)
10. Member of
Program Committee, Sixth International Parallel Processing Symposium, Beverly
Hills, California, March 23-26, 1992. (Sponsored by IEEE Computer Society)
11. Member of
Program Committee, Second IEEE Conference on Data Compression, Snowbird, Utah,
March 1992. (Sponsored by IEEE Computer Society)
13. Member of
Program Committee, Third IEEE Conference on Data Compression, Snowbird, Utah,
March 1993. (Sponsored by IEEE Computer Society)
14. Member of
Program Committee, Fourth IEEE Conference on Data Compression, Snowbird, Utah,
March 1994. (Sponsored by IEEE Computer Society)
15. Member of
Advisory Committee, Workshop of Parallel Algorithms (WOPA),1994.
16. Member of
Program Committee, Second International Conference on Massively Parallel
Processing Using Optical Interconnects (MPPOI1995)
19. Member of
Program Committee, IEEE Data Compression Conference(DCC95)
20. Member of
Program Committee, 1st Annual Meeting on DNA Based Computers(1995)
21. Member of
Program Committee, Workshop On Randomized Parallel Computing, 10th
International Parallel Processing Symposium (IPPS '96).
22. Member of
Program Committee, 8th Annual ACM Symposium on Parallel Algorithms and
Architectures(SPAA96)
23. Member of
Program Committee, IEEE Data Compression Conference(DCC96)
24. Member of
Program Committee, 2nd Annual Meeting on DNA Based Computers(1996)
25. Member of
Program Committee, 3rd annual IEEE Conference on Massively Parallel Processing
Architectures using Optical Interconnections (MPPOI'96)
26. Member of
Program Committee, IEEE Data Compression Conference(DCC97).
27. Member of
Program Committee, 3rd Annual Meeting on DNA Based Computers(1997).
28. Member of
Program Committee, Workshop On Randomized Parallel Computing, 11th
International Parallel Processing Symposium (IPPS '97).
29. Member of
Program Committee, DIMACS Workshop on "Randomization Methods in Algorithm
Design", Dec. 12-14, 1997, Princeton University. Probability.
30. Member of
Program Committee, 4th International Symposium on Solving Irregularly
Structured Problems in Parallel (IRREGULAR'97) University of Paderborn,
Germany, 11-13 June 1997.
31. Member of Program
Committee for the Algorithms and Applications track of 26th International
Conference on Parallel Processing (ICPP97) August 11-15, Indian Lakes Resort in
Bloomingdale, IL.
32. Member of Program
Committee for the IEEE International Conference On Robotics And Automation,
1997.
33. Member of Organizing
Committee, 4rth Annual Meeting on DNA Based Computing (1998).
34. Member of Program
Committee, vIEEE Data Compression Conference(DCC98), Snowbird, Utah, 1998.
35. Member of Advisory
Committee, Workshop on Parallel Algorithms (WOPA), 1998.
36. Member of Advisory
Committee, 1999 Workshop on Algorithms and Data Structures (WADS'99) August
12-14, 1999 Vancouver, British Columbia, Canada.
37. Program Chair, Workshop
in Biomolecular Computation: Its Potential and Applications, NSF, Arlington VI,
Oct 1, 1999.
38. Member of Program
Committee, IEEE Data Compression Conference(DCC99), Snowbird, Utah, 1999.
39. Member of Program
Committee, Workshop on Algorithms and Data Structures (WADS1999).
40. Co-Organizer of East
Coast Computer Algebra Day(ECCAD'99), NC State, Raleigh, NC, April 24, 1999.
41. Member of Program
Committee, Workshop on Algorithmic Foundations of Robotics (WAFR2000).
42. Member of Executive
Committee, DNA Based Computers, 2000.
43. Team Leader (with M.
Morf) for DNA/Biological SRC meeting ADT Novel Technologies for Information
Processing:, San Jose CA, (March 26, 2000).
43. Member of Program
Committee, Seventh DNA Based Computers, June 2001.
43. Panel Moderator:
Critical Assessment of Techniques for Microarray Data Analysis (CAMDA2000
Conference), Duke University, Durham, NC, 2001
44. Member of Organizing
Committee, Special session on Molecular Evolutionary Computing, 2001 Congress
on Evolutionary Computation (CEC2001) Seoul, Korea during May 27-30, 2001. at
CEC2001.
45. Member of Program
Committee, Seventh International Meeting on DNA Based Computers (DNA7), Tampa,
FL, June 11-13, 2001.
46. Chairman of Program
Committee, Symposium on Theory of Computing (STOC2002), May, 2002.
47. Member of Program
Committee, track on Biomolecular Computing and Quantum Computing at Genetic
& Evolutionary Computation Conference Conference (GECCO 03), Chicago, IL,
July 2002.
48. co-Chairman of Program
Committee, Ninth International Symposium on DNA Based Computers (DNA9),
Madison, Wisconsin, June, 2003.
49. Program
Chairman of the First Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO04), Snowbird, Utah, (April
21-23, 2004).
50. Member of
the Godel Prize Committee, ACM SIGACT, 2004-2005.
51. Member of Program
Committee, Fourth IEEE International Workshop on High Performance
Computational Biology (HiCOMB 2005).
52. Program
Chairman of the Second Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO05), Snowbird, Utah, (April
24-28, 2005).
53. Program
coChairman of the NSF Workshop: Emerging Opportunities of Nanoscience to
Energy Conversion and Storage, Arlington VI, November 21-22, 2005.
54. Member of
the Godel Prize Committee, ACM SIGACT, 2005-2008.
55. Member of Program
Committee, 18th ACM Symposium on Parallelism in Algorithms and
Architectures(SPAA06), Cambridge, MA, July 30 - August 2, 2006.
56. Program
Chairman of the Third Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO06), Snowbird, Utah, (April
23-27, 2006).
57. Member of
the Program Committee (for Programmable self assembly) of 2006
Robotics Science and Systems Conference (RSS 2006), University of Pennsylvania,
Philadelphia, PA, August 16th-19th, 2006.
58. Chair of the Godel
Prize Committee, ACM SIGACT, 2006-2007.
59. Program
Chairman of the Fourth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO07), Snowbird, Utah, (April
18-21, 2007).
60. General
Chairman of the Fifth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO08), Snowbird, Utah, (April
25-28, 2008).
61. Member of Committee for
NSF Bio-inspired Molecular Computing and Self-Assembly Thrust, Princeton, BC
2008.
62. Member of Steering
committee of International Conference on Bioinformatics and Computational
Biology (BICoB09), New Orleans, Louisiana USA (March 25-27, 2009).
63. General
Chairman of the Sixth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO09), Snowbird, Utah, (April
20-24, 2009).
64. Member
of Program Committee of Sixteenth Annual International Symposium on
DNA Based Computers (DNA16) Hong Kong, China (June 2010).
65. Member of Advisory
Board of Series on Computer Science and Computer Security for Higher Education
Press of Ministry of Education of China and Springer (2009-present).
66. Member of Program
Committee of International International Colloquium on Automata, Languages, and
Programming(ICALP), 2010 Track A
67. General
Chairman of the Seventh Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO10), Snowbird, Utah, (April
27-30, 2010).
68. General
Chairman of the Eighth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO11), Snowbird, Utah, (April
11-15, 2011).
69. Member of Program
Committee of Seventeenth Annual International Symposium on DNA Based
Computers (DNA17), Pasadena, CA (June 2011).
70. General
Chairman of the Ninth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO12), Snowbird, Utah, (April
16-19, 2012).
71. Member
of Program Committee of Eighteenth Annual International Symposium on
DNA Based Computers (DNA18), Aarhus, Denmark (June 2012).
72. General
Chairman of the Tenth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO13), Snowbird, Utah, (April
15-18, 2013).
73. Member
of Program Committee of Nineteenth Annual International Symposium on
DNA Based Computers (DNA19), Tempe, AZ (Aug 2013).
74. General
Chairman of the Eleventh Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO14), Snowbird, Utah, (April
14-17, 2014).
75. Member
of Program Committee of 20th Annual International Symposium on DNA
Based Computers (DNA20), Kyoto, Japan (Sept 2014).
76. General
Chairman of the 12th Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO15), Snowbird, Utah, (April
13-16, 2015).
77. Member
of Program Committee of 21th Annual International Symposium on DNA
Based Computers (DNA21), Cambridge, MA (Aug 2015).
78. General
Chairman of the Eleventh Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO15), Snowbird, Utah, (April
13-16, 2015).
79. Member
of the Advisory Board of your Journal of King Abdulaziz
University Computing and Information Technology, 2013-2014.
80. General
Chairman of the Twelfth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO16), Snowbird, Utah, (April
11-14, 2016).
81. Member
of Program Committee of 22nd Annual International Symposium on DNA
Based Computers (DNA22), Ludwig-Maximilian-Universität,
Munich, Germany(Sept 2016).
82. General Chairman of
the Thirteenth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices (FNANO17), Snowbird, Utah, (April 10-13, 2017).
83. Member
of Program Committee of 23rd Annual International Symposium on DNA
Based Computers (DNA23), University of
Texas at Austin, Austin, Texas, USA(Aug 2017).
84. General
Chairman of the Fourteenth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO18), Snowbird, Utah, (April
16-19, 2018).
85. Member
of Program Committee of 24th Annual International Symposium on DNA
Based Computers (DNA24), Jinan, China (Aug 2018).
86. Member
of Program Committee of 25th Annual International Symposium on DNA
Based Computers (DNA25), Seattle, Washington (Aug 5-8, 2019).
87. Conference
Co-Chair 2019 IEEE International Conference on Bioinformatics and
Biomedicine(IEEE BIBM 2019), San Diego, CA, US, Nov 18-21, 2019.
88. General
Chairman of the Sixteenth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO19), Snowbird, Utah, (April
15-18, 2019).
89. General
Chairman of the Seventeenth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO19), Snowbird, Utah, (April 6-9,
2020).
90. Member of Faculty 1000
(member 2007-current)
91. Member of Steering
Committee of IEEE International Conference on Computations and Biomedical
Systems (IEEE CBS), since 2010-current.
92. Member of the DNA
Computing Steering Committee, 2001-current.
93. Member of the ISNSCE
Council, 2006-current.
94. Chair of ISNSCE
Scientific Advisory Council, 2006-current.
95. Member
of Advisory Board of Wiley Book Series on Nature Inspired Computing,
2009-present
Courses Taught
Spring, 2024, Molecular
Assembly and Computation, COMPSCI 590d, Duke University.
Fall, 2023, History of
Computing, Cryptography, and Robotic Devices, COMPSCI 093, Duke University.
Spring, 2023, Computational
Complexity, COMPSCI 534, Duke University
Fall, 2022, Introduction to
Algorithms, COMPSCI 531, Duke University.
Spring, 2022, Molecular
Assembly and Computation, COMPSCI 590.10, Duke University.
Fall, 2021, History of
Computing, Cryptography, and Robotic Devices, COMPSCI 093, Duke University.
Spring, 2021, Computational
Complexity, COMPSCI 534, Duke University
Fall, 2020, Introduction to
Algorithms, COMPSCI 531, Duke University.
Spring, 2020, Molecular
Assembly and Computation, COMPSCI 590.03, Duke University.
Fall, 2019, Algorithm
Paradigms, COMPSCI 530, Duke University
Spring, 2019, Computational
Complexity, CPS 531, Duke University
Fall, 2018, Algorithm
Paradigms, COMPSCI 530, Duke University
Spring, 2018, Molecular
Assembly and Computation, COMPSCI 590.01, Duke University.
Fall, 2017, Algorithm
Paradigms, COMPSCI 530, Duke University.
Spring, 2017, Computational
Complexity, CPS 531, Duke University.
Fall, 2016, Algorithm
Paradigms, COMPSCI 530, Duke University
Spring, 2016, Molecular
Assembly and Computation, COMPSCI 590.01, Duke University.
Fall, 2015, Algorithm
Paradigms, COMPSCI 530, Duke University.
Spring, 2015, Computational
Complexity, CPS 531, Duke University.
Fall, 2014, Algorithm
Paradigms, COMPSCI 530, Duke University.
Fall, 2013, Algorithm
Paradigms, COMPSCI 530, Duke University.
Spring, 2012, Molecular
Assembly and Computation, COMPSCI 590.02, Duke University.
Fall, 2011, Analysis of
Algorithms, CPS 130, Duke University.
Spring, 2011, Computational
Complexity, CPS 240, Duke University.
Fall, 2010, Analysis of
Algorithms, CPS 130, Duke University.
Spring,
2010. Alternative Computational Models, Spring 2010.
Fall, 2009, Analysis of
Algorithms, CPS 130, Duke University.
Spring, 2009, Computational
Complexity, CPS 240, Duke University.
Fall, 2008, Analysis of
Algorithms, CPS 130, Duke University.
Spring, 2008, Randomized
Algorithms, CPS 237, Duke University.
Fall, 2007, Analysis of
Algorithms, CPS 130, Duke University.
Spring, 2007, Computational
Complexity, CPS 240, Duke University.
Fall, 2006, Analysis of
Algorithms, CPS 130, Duke University.
Spring, 2006, Randomized
Algorithms, CPS 237, Duke University.
Fall, 2005, Analysis of
Algorithms, CPS 130, Duke University.
Summer, 2005, Analysis
of Algorithms(NCSC 6021). Taught this masters-level remote instructional
course for National Technical University(Walden University), produced at MGM
Studios, Orlando, FL, June, 2005.
Spring, 2005, Analysis of
Algorithms, CPS 130, Duke University.
Fall, 2004, Efficient
Algorithms, CPS 230, Duke University.
Spring, 2003, Analysis of
Algorithms, CPS 130, Duke University.
Fall, 2002, Efficient
Algorithms, CPS 230, Duke University.
Spring, 2002, Randomized
Algorithms, CPS 237, Duke University.
Fall 2001, Analysis of
Algorithms, CPS 130, Duke University.
Spring 2001, Mathematical
Foundations of Computer Science, CPS 140, Duke University.
Fall 2000, Computational
Biology, CPS 296.2, Duke University.
Spring 2000, Computational
Biology and Biomolecular Computation, CPS 296.2, Duke University.
Fall 1999, Analysis of
Algorithms, CPS 130, Duke University.
Spring 1999, Analysis of
Algorithms, CPS 130, Duke University.
Fall 1998, Parallel
Algorithms, CPS 236, Duke University.
Spring 1998, Analysis of
Algorithms, CPS 130, Duke University.
Fall 1997, Design and
Analysis of Algorithms, CPS 230, Duke University.
Spring 1997, Analysis of
Algorithms, CPS 130, Duke University.
Fall 1996, Design and
Analysis of Algorithms, CPS 230, Duke University.
Spring 1996, Parallel
Algorithms, CPS 236, Duke University.
Fall 1995, Analysis of
Algorithms, CPS 130, Duke University.
Spring 1995, Parallel
Algorithms, CPS 236, Duke University.
Fall 1994, Analysis of
Algorithms, CPS 230, Duke University.
Fall 1993, Analysis of
Algorithms, CPS 174, Duke University.
Spring 1993, Parallel
Algorithms, CPS 230, Duke University.
Fall 1992, Analysis of
Algorithms, CPS 174, Duke University.
Spring 1992, Numerical and
Algebraic Algorithms, CPS 206, Duke University.
Fall 1991, Parallel
Algorithm Implementation, CPS 265, Duke University.
Spring 1991, Computational
Robotics, CPS 265, Duke University.
Fall 1990, Analysis of
Algorithms, CPS 174, Duke University.
Spring 1990, Advanced
Topics in Theory, CPS 265, Duke University.
Fall 1989, Analysis of
Algorithms, CPS 224, Duke University.
Spring 1989, Advanced
Topics in Massively Parallel Processing, CPS 265, Duke University.
Spring 1989, Advanced
Topics in Algorithms, CPS 265, Duke University.
Fall 1988, Analysis of
Algorithms, CPS 174, Duke University.
Spring 1988, Parallel
Algorithms, CPS 265, Duke University.
Fall 1987, Analysis of
Algorithms, CPS 224, Duke University.
Spring 1987, Parallel
Algorithms, CPS 265, Duke University.
Fall 1986, Analysis of
Algorithms, CPS 224, Duke University.
Spring 1994, Algorithms for
Scientific Computation CS 15-850, Carnegie-Mellon University.
Fall 1985, Introduction to
the Theory of Computing, CS 207, Harvard University.
Spring 1985, The Complexity
of Computations: Parallel Computation, CS 224, Harvard University.
Spring 1984, The Complexity
of Computations: Parallel Computation, CS 224, Harvard University.
Fall 1983, Efficient
Algorithms, CS 226, Harvard University.
Spring 1983, The Complexity
of Computations: Parallel Computation, AM 224, Harvard University.
Fall 1982, Efficient
Algorithms, AM 226, Harvard University.
Spring 1982, The Complexity
of Computations: Parallel Computation, AM 224, Harvard University.
Fall 1981, Introduction to
the Theory of Computing, AM 207, Harvard University.
Spring 1981, Data
Structures, AM 119, Harvard University.
Fall 1980, Introduction to
the Theory of Computing, AM 207, Harvard University.
Spring 1980, Introduction
to the Theory of Computing, AM 207, Harvard University.
Fall 1979, Efficient
Algorithms, AM 226, Harvard University.
Spring 1979, Seminar in
Research Topics, CSC 589, University of Rochester.
Fall 1978, Introduction to
Theory of Computation, CSC 281/481, University of Rochester.
Fall 1978, Programming
Problems Seminar, CSC 400, University of Rochester.
Spring 1978, Seminar on
Optimization of Computer Programs, CSC 589, University of Rochester.
Fall 1977, Programming
Problems Seminar, CSC 400, University of Rochester.
Recent
Invited Talks
Biomolecular Computation by
Local Assembly, University of Delaware, Mathematics Dept, April 19, 1997
Biomolecular Computation by
Local Assembly, U Pennsylvania, April 18, 1997
Biomolecular Computation,
Ultrascale Meeting, DARPA, Estes Park, CO, Oct 14, 1997.
Biomolecular Computation
(Distinguished Lecture Series), Department of Computer Science, Rice
University, April 30, 1997
Approximate Complex
Polynomial Evaluation, Department of Computer Science, U. of Houston, May 1,
1997
Randomized parallel
algorithms in computational geometry, October 10, 1997, School and Workshop on
Randomized Algorithms in Sequential, Parallel, and Distributed Computing(RALCOM
97),Santorini Island, Greece.
Randomized parallel
algorithms for routing and sorting October 11, 1997, Workshop on Randomized
Algorithms in Sequential, Parallel, and Distributed Computing(RALCOM 97),
Santorini Island, Greece.
Biomolecular Computation,
CS Dept, Brandeis University, Nov 22, 1997.
Toward
Autonomous Robots: Robust, Adaptive and Dynamic Motion, 19 NSF Design and
Manufactoring Grantees Conference, Monterrey, Mexico, Jan 1998.
Paradigms for Biomolecular
Computation, First International Conference on Unconventional Models of
Computation, Auckland, New Zealand, January 1998. in Unconventional Models of
Computation, edited by C.S. Calude, J. Casti, and M.J. Dinneen, Springer Publishers,
January 1998, pp. 72-93.
Microflow Bio-Molecular Computation, 4th DIMACS Workshop on DNA Based Computers, University of
Pennsylvania, June, 1998.
Nano-Robotics
Motion Planning and Its Applications in Nanotechnology and Biomolecular
Computing, NSF Design and Manufacturing Grantees
Conference, Longbeach, CA, Jan 5-8, 1999.
Quantum
Information Processing: Compression, Coding, and Related Computations, Plenary
Talk, IEEE Data Compression Conference (DCC'99)
Snowbird, Utah, March 29 - 31, 1999.
Experimental Progress in
Computation by Self-Assembly of DNA Tilings, 5th DIMACS
Workshop on DNA Based Computers, MIT, June 14, 1999.
DNA-based
Cryptography, 5th DIMACS Workshop on DNA Based Computers,
MIT, June 15, 1999.
Molectronics
Software Architecture, DARPA
Molelectronics Meeting, Ashburn, VI, July8-9, 1999.
DNA Cryptosystems, Workshop in
Biomolecular Computation: Its Potential and Applications, NSF, Arlington VI,
Oct 1, 1999, (abstract).
Collaborative Biomolecular Computation Projects in Europe,
Japan, & the US, Workshop in
Biomolecular Computation: Its Potential and Applications, NSF, Arlington VI,
Oct 1, 1999, (abstract).
Nonparametric
Multiscale Multimodal Model for Detection/Recognition, Multi-Modality Image Fusion Conference, Rochester, NY, Oct
7, 1999.
Software Architecture for a Molecular Computer, DARPA, Arlington VI, Nov 30, 1999.
Molectronics Software
Architecture, Center Nanoscale Science and Technology, Rice University, Dec 3,
1999.
DNA Cryptosystems, Invited
Talk, National Security Agency(NSA), Fort Meade, Maryland, Dec 13, 1999.
Associative Search in DNA Databases, Invited
Talk, National Reconnaissance Office (NRO),
Chantilly, VA, Dec 14, 1999.
Software Design for
Molectronics, DARPA Molectronics Meeting, Arlington, VI,
(Feb 26,2000).
An
Efficient Approximation Algorithm for Weighted Region Optimal Path Problem, Workshop on Foundations of Robotics (WFR2000), Dartmouth, NH,
(March 17, 2000).
Self-Assembled DNA
Nanostructures, ADT Novel Technologies for Information:
DNA/Biological SRC meeting, San Jose CA, (March 26, 2000).
Self-Assembled
DNA Nanostructures, NSF workshop on
nano-scale molecular based electronics, Arlington, VI, (May 18, 2000).
Computationally
Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using
Error-Correcting Codes and Vector-Quantization, Invited
Talk, Sixth International Meeting on DNA Based
Computers (DNA6), Leiden, The Netherlands, (June 14, 2000)
Challenges
and Applications for Self-Assembled DNA Nanostructures, Plenary Talk, Sixth International Meeting on DNA Based Computers (DNA6), Leiden,
The Netherlands, (June 16, 2000)
Algorithmic
self-assembly of DNA Tilings, City University
of Hong Kong, Kowloon, Hong Kong, Oct 2, 2000.
Improved
DNA Synthesis and Associative Search Using Error-Correcting Codes and
Vector-Quantization, City University
of Hong Kong, Kowloon, Hong Kong, Oct 3, 2000.
On the
Impossibility of Interaction-Free Quantum Sensing for Small I/O Bandwidth, City University of Hong Kong, Kowloon, Hong Kong, Oct 4,
2000.
A Biomolecular System for Ultra-Scale Associative Search, Invited
Talk, National Reconnaissance Office(NRO), Chantilly, VA, November, 2000.
A
Biomolecular System for Ultra-Scale Associative Search, Theory Seminar, CS Dept, Duke University, Durham, NC,
November 16, 2000.
Experimental Demonstrations
of Ultra-Scale Molecular Data Storage & Retrieval, Computation and
Assembly, Information Science and Technology Colloquium Series Invited Talk,
NASA Goddard, Maryland, Jan 17, 2001.
Programmable
Assembly at the Molecular Scale: Self-Assembly of DNA Lattices, Plenary Talk, 2001 IEEE International Conference on Robotics and Automation
(ICRA2001), Seoul, Korea, May 26, 2001
Molecular
Computing via Programmed Self-Assembly of Patterned Molecules, Plenary Talk, 2001 Congress on Evolutionary Computation (CEC2001), Seoul, Korea,
May 28, 2001
Experimental
Construction of Very Large Scale DNA Databases with Associative Search
Capability, Seventh International Meeting on DNA Based
Computers (DNA7), Tampa, FL, June 11-13, 2001.
Molecular
Database Systems for Storage, Processing & Retrieval of Genetic Information
& Material, Invited Talk, MiniSymposium
"On Interfaces among Information Technology, sensing sciences, and
Biological Systems", organized by Jagdish Chandra and Srikanta Kumar, SIAM
Annual Meeting, San Diego, California, July 9-13, 2001
Movement
Planning in the Presence of Flows, Workshop
on Algorithms and Data Structures (WADS2001), Brown
University, Providence, RI, August 8-10, (2001).
Computations
& patterned structures via DNA self-assembly, Invited
talk, Max Planck Institute for the Physics of
Complex Systems, Dresden, Germany, August 20-24,2001.
DNA in
NanoScience, Invited talk, Department of
Computer Science Seminar Series, Duke University, Durham, NC, October
22, 2001
DNA
Computation by Self-Assembly of DNA Nano-Scale Structures, Symposium on New
Approaches toward Computing, Plenary Talk, National Academy of
Arts and Sciences, Brussels, Belguim, November 9, 2001
Programmable
DNA Lattices: Design, Synthesis and Applications, Invited
Talk, Joint DARPA/NSF BioComp PI Meeting, Monterey
Bay, CA. November, 27 - 30, 2001.
Self-Assembly
of DNA Nano-Scale Structures for Computation, Invited
Talk, Joint DARPA/NSF BioComp PI Meeting, Monterey
Bay, CA. November, 27 - 30, 2001.
Self-Assembly
of DNA Nano-Scale Structures, Invited Talk, DARPA ITO BioComp
PI Meeting, Washington, DC, May 22-24, 2002.
DARPA
Supplemental Project Overview, Invited Talk, Central
Intelligence Agency(CIA), McLean, VI, Feb 12, 2002.
DNA Database Project Final
Report Talk, National
Reconnaissance Office(NRO), Chantilly, VA, Feb 12, 2002.
The
Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA, The
8th International Meeting on DNA Based Computers (DNA 8), Sapporo, Japan,
June 10-13, 2002.
Molecular Assembly and Computation: From Theory
to Experimental Demonstrations, Plenary Talk, 29th
International Colloquium on Automata, Languages, and Programming(ICALP),
Málaga, Spain (July 8, 2002).
Programmable Molecular
Self-Assembly: Theory and Experimental Demonstrations, invited talk, Alternative Computing
Workshop, Mathematics in Nanoscale Science and Engineering, UCLA, September 30, 2002.
Programmable Molecular Self-Assembly: Theory and Experimental
Demonstrations, distinguished lecture, Computer Science
Department, John Hopkins University, Baltimore, Maryland, October 3,
2002.
DARPA Supplemental Project Overview
Talk & Demonstration, MITRE Corporation,
McLean, VI, October 4, 2002
Programmable
DNA Lattices: Design, Synthesis and Applications, Invited
Talk, Department of Computer Science, Boston
University, Boston, MA, December 2, 2002.
Patterned Molecular
Self-Assembly, Invited Talk, Joint DARPA/NSF
BioComp PI Meeting, San Deigo, CA. December 7, 2002.
DARPA Supplemental Project
Overview Talk & Demonstration, MITRE Corporation, McLean,
VI, April 14, 2003
DNA Nanostructures:
Patterning and Computation, Duke Nanostructure Workshop, Duke University,
Durham, NC, May 5, 2003
Achieving
Patterned Molecular Self-Assembly, Invited Talk, DARPA
BioComp PI Meeting, Fort Lauderdale, Florida, May 15,
2003.
Directed Nucleation
Assembly of Barcode Patterned DNA Lattices, DNA9
Conference, Madison, Wisconsin, June 2, 2003
Programmable DNA Lattices:
Design, Synthesis and Applications, Keynote Talk, 5th Conference on
Computational Biology and Genome Informatics (CBGI), 7th Joint Conference on
Information Sciences (JCIS 2003), September 26-30,2003. Cary, NC, USA.
Compact Error-Resilient
Computational DNA Tiling Assemblies, Tenth International Meeting
on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.
Designs for Autonomous
Unidirectional Walking DNA Devices, Tenth International Meeting
on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.
Design of an Autonomous DNA
Nanomechanical Device Capable of Universal Computation and Universal
Translational Motion, Poster Presentation, Tenth International Meeting
on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.
TileSoft: Sequence
Optimization Software For Designing DNA Secondary Structures, Poster
Presentation, Tenth International Meeting on DNA Based Computers
(DNA10), Milano, Italy, June 7-10, 2004.
DNA-Based Nano-Engineering:
DNA and its Enzymes as the Engines of Creation at the Molecular
Scale, Plenary Invited Talk, Tenth International Meeting on DNA
Based Computers (DNA10), Milano, Italy, June 7-10, 2004.
Design, Simulation, and
Experimental Demonstration of Self-Assembled DNA Nanostructures and DNA Motors,
Invited Talk, Computational Modeling and Simulation of Materials (CIMTEC)
Conference, Acireale, Sicily, Italy, May 29-June 4, 2004.
Molecular Computations
Using Self-Assembled DNA Nanostructures and Autonomous Motors, Invited Talk,
Bio-inspired Computing Track, Unconventional Programming Paradigms (UPP),
Mont Saint-Michel, France, September 15–17, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Korean Society for Bioinformatics Conference, Seoul, South Korea,
November 5, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Nano System Institute (NSI_NCRC), Seoul National University, Seoul, South
Korea, November 8, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Biomedical MEMS Laboratory, Korea Institute of Science and
Technology (KIST), Seoul, South Korea, November 8, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Division of Nano Science, Ewha Woman’s University, Seoul, South Korea,
November 9, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Department of BioSystems, Korean Advanced Institute of Science and
Technology (KAIST), Taejon, South Korea, November 9, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Department of Materials Science and Engineering, Massachusetts Institute
of Technology (MIT), Cambridge, MA, December 6, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Department of Chemistry, Tufts University, Medford, MA, December 7, 2004.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Workshop on Engineering a DNA World, Center for Biological Circuit
Design, California Institute of Technology (Caltech), Pasadena, CA, January
6-8, 2005.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Departments of EE and Material Science, Seattle, WA, February 15, 2005.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited
Talk, Frontiers 2005, Duke University, Durham, NC, May 4, 2005.
Complexity of Graph
Self-Assembly in Accretive Systems and Self-Destructible Systems, Eleventh
International Meeting on DNA Based Computers (DNA11), London, Ontario,
June, 2005.
Design of Autonomous DNA
Cellular Automata, Eleventh International Meeting on DNA Based
Computers (DNA11), London, Ontario, June, 2005.
A Self-Assembly Model of
Time-Dependent Glue Strength, Eleventh International Meeting on DNA
Based Computers (DNA11), London, Ontario, June, 2005.
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Transport,
Invited Talk, New York Academy of Science, New York, NY, Oct 11, 2005.
Design and Simulation of
Self-Repairing DNA Lattices, 12th International Meeting on DNA Computing (DNA
12), Seoul, Korea, June 5-9, 2006.
On Constructing Tile-less
DNA Ribbons and Tubes, 12th International Meeting on DNA Computing (DNA 12),
Seoul, Korea, June 5-9, 2006.
Capabilities and Limits of
Compact Error Resilience Methods for Algorithmic Self-Assembly in Two and Three
Dimensions, 12th International Meeting on DNA Computing (DNA 12), Seoul, Korea,
June 5-9, 2006.
DNA Modeller: Modeling DNA
based Molecular Systems, Poster Abstract, 12th International Meeting on DNA Computing
(DNA 12), Seoul, Korea, June 5-9, 2006. (Poster Abstract).
Self-Assembled DNA
Nanostructures for Molecular Scale Patterning, Computation and Transport,
Invited Talk, 14th Workshop on Logic, Language, Information and
Computation (WoLLIC'2007), Rio de Janeiro, Brazil, July 2-5, 2007.
DNA Self-assembly and
Autonoumous R Molecular Robots. Invited Talk, presented at
the Conference on Morphological Computation, Venice, Italy, March 26-28,
2007.
Autonomous Programmable
Biomolecular Devices Using Self-Assembled DNA Nanostructures, invited
talk, Fourteenth Workshop on Logic, Language, Information and Computation
(WoLLIC'2007), Rio de Janeiro, Brazil, July 2-5, 2007.
Autonomous Programmable DNA
Nanorobotic Devices Using DNAzymes, 13th International Meeting on DNA
Computing (DNA 13), Memphis, Tennessee, June 4-8, 2007.
Activatable Tiles for
Compact Error-Resilient Directional Assembly. 13th International Meeting
on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8, 2007.
Autonomous Programmable
Biomolecular Devices Using Self-Assembled DNA Nanostructures, invited talk,
Workshop on Algorithmic Bioprocesses, Lorentz Center, Leiden University,
Leiden, Netherlands, Dec 3-7, 2007.
Autonomous Programmable
Biomolecular Devices Using Self-Assembled DNA Nanostructures, invited talk,
joint talk, University of Vancouver & Simon-Fraser University, Vancouver,
BC, Jan 30, 2008.
Isothermal Reactivating
Whiplash PCR for Locally Programmable Molecular Computation, Fourteenth
International Meeting on DNA Based Computers (DNA14), Prague, Czech
Republic (June, 2008).
Programmable DNA
Nanodevices, NSF EMT 2008 Workshop, Princeton, NJ, July 24-25, 2008.
DNA Nanoassembly and DNA
Nanodevices: Challenges, Applications and Research Progress, DNA-based
nanotechnology: Construction, mechanics, and electronics, International
Workshop, Dresden, Germany, (May 11 - 15, 2009).
DNA nanoassembly and DNA
Nanodevices: Challenges, Applications and Research Progress, Future and
Emerging Technologies (FET) seminar, European Commission, Brussels, Belgium,
(May 20, 2009).
Design of a Biomolecular
Device that Executes Process Algebra, Fifteenth International Meeting on
DNA Computing and Molecular Programming (DNA15), Fayetteville,
Arkansas (June 8-11, 2009).
The Tile Complexity of
Linear Assemblies, 36th International Colloquium on Automata, Languages and
Programming (ICALP 2009), Rhodes, Greece (July 5 - 12, 2009).
DNA Nanoassembly and DNA
Nanodevices: Challenges, Applications and Research Progress, Computer
Technology Institute, University of Patras, Patras, Greece (July 19,
2009).
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Wuhan University. Hubei, China, May 17, 2010.
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Hefei University of Technology, Hefei, China, May
18, 2010.
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Anhui University, Hefei, China, May 18, 2010.
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, North China University of Technology, Beijing,
China, May, 2010.
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, College of Computer Science and Information
Technology, Kunming Normal University, Kunming, China, June 1 2010.
The Theory of
Self-Assembly, Tuitorial, International Conference on DNA Computing and
Molecular Programming, (DNA16), Hong Kong University of Science and Technology.
Hong Kong, China, June 14, 2010.
High-Fidelity DNA
Hybridization using Programmable Molecular DNA Devices, International
Conference on DNA Computing and Molecular Programming, (DNA16), Hong Kong
University of Science and Technology. Hong Kong, China, June 14-17th,
2010.
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation,
Bioengineering Seminar Series, Hong Kong University of Science and Technology
(HKUST), Department of Chemical and Biomolecular Engineering, Hong Kong, China,
June 18. 2010.
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation,
Chinese University of Hong Kong, Hong Kong, China, June 18. 2010.
DNA-Based Assembly of
Molecular-Scale Autonomous Devices for Sensing, Transport and Computation,
Distinguished Lecture, North Eastern University, College of Computer Science,
Boston, MA, November 18, 2010.
DNA-Based Molecular Devices, Keynote talk ICCABS, Orlando, FL, Feb. 3‐5,
2011.
DNA Self-Assembled
Autonomous Devices for Programmed Molecular Computation, Transport, and
Amplified Sensing, van Leeuwenhoek Lecture on BioScience, Leiden
University, Leiden, Netherlands, May 26 2011.
Programmable Self-Assembled
DNA-Based Autonomous Molecular Devices, Microsoft Research, Cambridge,
June 2, 2011.
Programmable Self-Assembled
DNA-Based Autonomous Molecular Devices, Department of Physics, Clarendon
Laboratory, University of Oxford, Oxford University, UK, June 7, 2011.
Localized Hybridization
Circuits, International Conference on DNA Computing and Molecular Programming,
(DNA17), California Institute of Technology, Pasadena, California, Sept 19-23,
2011.
Programmable Self-Assembled
DNA-Based Autonomous Molecular Devices, Faculty of Computing and
Information Technology (FCIT), King Abdulaziz University (KAU), Jeddah, Saudi
Arabia, December 4, 2011.
Development and
Demonstration of an Energy-Efficient Cost-Effective Durable Solar
Concentrator, Faculty of Computing and Information Technology (FCIT), King
Abdulaziz University (KAU), Jeddah, Saudi Arabia, December 11, 2011.
Development and
Demonstration of an Energy-Efficient Cost-Effective Durable Solar
Concentrator, King Abdullah City for Atomic and Renewable Energy (KACARE),
Riyadh, Saudi Arabia, December 13, 2011
Programmable Self-Assembled
DNA-Based Autonomous Molecular Devices, Effat
University, Jeddah, Saudi Arabia, May 13, 2012.
Development and
Demonstration of an Energy-Efficient Cost-Effective Durable Solar Concentrator
for Powering Desalination, King Abdullah City for Atomic and Renewable
Energy (KACARE), Riyadh, Saudi Arabia, Sept 16, 2012.
Development and
Demonstration of an Energy-Efficient Cost-Effective Durable Solar Concentrator
for Powering Desalination, Saudi Arabian Ministry of Water and
Electricity, Riyadh, Saudi Arabia, Sept 16, 2012.
Keynote Talk, Future
Challenges for DNA-Based Nano-Architectures and Nano-Devices, Workshop on
Molecular Programming and Computing, Copenhagen, Denmark, May 2-4, 2013.
Keynote talk, 4th IEEE
International Conference on Computational Advances in Bio and Medical Sciences
(ICCABS), Miami Beach Resort and Spa, Miami Beach, FL, June 2-4, 2014.
DNA Computing: Theory,
Experiments & Software, Computability in Europe: Evolving
Computability (CiE 2015), Bucharest, Romania, July 2, 2015.
Self-Assembled DNA
Nanostructures, Computability in Europe: Evolving Computability (CiE
2015), Bucharest, Romania, July 3, 2015.
DNA-Based Programmable
Autonomous Molecular Robotic Devices, Computability in Europe: Evolving
Computability (CiE 2015), Bucharest, Romania, July 4, 2015.
DNA-Based Molecular
Assembly and Computation, Dagstuhl Seminar 15402 Self-assembly and
Self-organization in Computer Science and Biology, Sept 27-October 02, Dagstuhl
Saarbrücken, Germany, July 2, 2015.
DNA-Based Programmable
Autonomous Molecular Devices, MSE Department, Boise
State University, Boise, ID, October 30, 2015.
DNA-Based Programmable
Autonomous Molecular Devices, Chemistry Department, UNC
Charlotte, NC, October 20, 2016.
DNA-Based Programmable
Autonomous Molecular Devices, Chemistry
Department, University of New Mexico, Albuquerque, May 3, 2017.
Applications of DNA
Nanodevices in Cancer Cell Detection, Computer Science and Engineering Dept,
Nile University, Al Sheikh Zayed, Giza Governorate, Egypt, May 2,
2019.
Applications of DNA
Nanodevices in Cancer Cell Detection, Computer Science and Engineering
Depts, Faculty of Electronic Eng., Menoufia University, Al
Minufya, Egypt, May 5, 2019.
Applications of DNA
Nanodevices in Cancer Cell Detection, Nanotechnology Research Centre (NTRC),
British University, El Sherouk, Cairo Governorate, Egypt, May 14, 2019.
Books
1. John H.
Reif (Editor), VLSI Algorithms and Architectures, 3rd Aegean Workshop on
Computing, AWOC 88, Corfu, Greece, June 28 - July 1 1988, 476
pages, Springer-Verlag Lecture Notes in Computer Science, Vol. 319 (1988).
2. John H.
Reif (Editor), Synthesis
of Parallel Algorithms, 22 chapters, 1011 pages. Kluwer
Academic Publishers, San Mateo, California, 1993.
3. Robert
Paige, John H. Reif, and Ralph Wachter (Editors), Parallel
Algorithm Derivation and Program Transformation, 228
pages. Published by Kluwer Academic Publishers, 1993.
4. Sanguthevar
Rajasekaran, pp. M. Pardalos, John H. Reif and J. Rolim (Editors), Handbook of Randomized
Computing (Edited by), Kluwer Volume I and II, Academic Press, London,
2001.
5. Proceedings of
the 34th ACM Symposium on Theory of Computing (STOC2002), (Edited
by John H. Reif), Montréal, Québec, Canada, May 19-21,
2002. Also, John H. Reif, Guest Editor, Special Issue of
Selected Papers from Proceedings of the Thirty-Fourth Annual ACM Symposium on
Theory of Computing (STOC2002) Journal of Computer and System Sciences(JCSS),
Volume 67, Issue 2, Page 211, (September 2003). Guest Editor’s Foreword,
Page 211. [PDF]
6. Junghuei Chen
and John H. Reif (Editors), Proceedings of the Ninth International
Meeting on DNA Based Computers (DNA9), Madison, Wisconsin, June 1-3,
2003, 225 pages, Lecture Notes in Computer Science Vol. 2943,
Springer-Verlag, New York, (2004).
7. John H. Reif (Editor),
Proceedings of the First Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO04), Snowbird, Utah, (April
21-23, 2004), Published by Sciencetechnica (2004). Editor’s
Foreword [PDF]
8. John H. Reif (Editor),
Proceedings of the Second Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO05), Snowbird, Utah, (April
24-28, 2005), Published by Sciencetechnica (2005). Editor’s
Foreword [PDF]
9. John H. Reif (Editor),
Proceedings of the Third Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO06), Snowbird, Utah, (April
23-27, 2006), Published by Sciencetechnica (2006).
10. John H. Reif (Editor),
Proceedings of the Fourth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO07), Snowbird, Utah, (April
18-22, 2007), Published by Sciencetechnica (2007).
11. Sanguthevar Rajasekaran and
John H. Reif (Editors), Handbook
of Parallel Computing: Models, Algorithms and Applications,
Published by Taylor & Francis, Boca Raton, FL.
ISBN 978-1584886235 (December, 2007). [PDF]
12. John H. Reif (Editor),
Proceedings of the Fifth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices(FNANO08), Snowbird, Utah, (April
21-25, 2008), Published by Sciencetechnica (2008).
13. John H. Reif and Marya
Lieberman, editors, Proceedings of the Sixth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO09), Snowbird, Utah,
Published by Sciencetechnica (April 20-24, 2009).
14. Sudheer Sahu and John
H. Reif, 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.
15. John H. Reif and Marya
Lieberman, editors, Proceedings of the Seventh Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO10), Snowbird, Utah,
Published by Sciencetechnica (April 27-30, 2010).
16. John H. Reif and Marya
Lieberman, editors, Proceedings of the Eighth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO11), Snowbird, Utah,
Published by Sciencetechnica, (April 11-15, 2011).
John H. Reif and Marya
Lieberman, editors, Proceedings of the Ninth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO12), Snowbird, Utah,
Published by Sciencetechnica, (April 16-19, 2012).
Papers (most are
downloadable)
10. Gary L.
Peterson and John H. Reif, Multiple-Person Alternation. 20th Annual
IEEE Symposium on Foundations of Computer Science, San Juan, Puerto Rico,
October 1979, pp. 348-363. Published as Gary L. Peterson, John H. Reif, and
Selman Azhar, Lower Bounds for Multiplayer Noncooperative Games of Incomplete
Information, Computers and Mathematics with Applications, Volume 41, April 2001,
pp. 957-992. [PDF]
42a Portions Published as
Parallel Tree Contraction Part I: Fundamentals, Parallel Tree Contraction
Part 1: Fundamentals. In Randomness and Computation, (Advances in Computing
Research, Vol. 5., Silvio Micali, editor), pp. 47–72, JAI Press,
Greenwich, Connecticut, 1989. [PDF]
42b Portions Published as
Parallel Tree Contraction Part II: Further Applications, SIAM Journal
on Computing, Vol. 20, No. 6, pp. 1128-1147, December 1991. [PDF]
138. John H.
Reif and James A. Storer, 3-Dimensional Shortest Paths in the Presence of
Polygonal Obstacles. 13th Symposium on Mathematical Foundations of
Computer Science, (Edited by Michal Chytil, Ladislav
Janiga, Václav Koubek) Czechoslovakia, August 29-September 2, 1988,
pp. 85-92. Published as A Single-Exponential Upper Bound for Finding Shortest
Paths in Three Dimensions. Journal of the ACM(JACM), Vol. 41, No.
5, Sept. 1994, pp. 1013-1019. [PDF]
247. Reem
Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu Bui, Tianqi Song, and John Reif,
Kinetic Digraph Rewrite Systems: Coarse-Grained Models for Dynamic DNA
Nanodevices, Poster Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013.
Also, A Python Implementation of a DNA Graph Rewriting System (DAGR),
poster abstract, FNANO2015, p148, April 2015. Published as Reem Mokhtar,
Sudhanshu Garg, Harish Chandran, Hieu Bui, Tianqi Song, and John Reif, Modeling
DNA Nanodevices Using Graph Rewriting Systems, invited
Chapter, Advances in Unconventional Computing, Volume
2: Prototypes, Models and Algorithms (Edited by Andrew Adamatzky), Springer, pp. 347-396 (2017). ISBN
978-3-319-33921-4 [PDF] [PDF]
248. Hieu
Bui, Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Harish Chandran, and John Reif,
Local Hybridization Chain-Reactions on the Surface of DNA Origami, Poster
Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013. Also Design DNA
Hairpin Systems for Localized DNA Hybridization Reactions, poster abstract,
FNANO2015, p169, April 2015. Expanded paper rewritten for journal publication
as: Hieu Bui, Sudhanshu Garg, Reem Mokhtar, Harish Chandran, Vincent
Miao and John Reif, Design and Analysis of Localized DNA
Hybridization Chain Reactions, Small (2017), 1602983. DOI: 10.1002/smll.201602983 [PDF] [PDF]
249. John
H. Reif and Tianqi Song, Complexity and Computability of Temperature-1 Tilings,
Poster Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013. Poster Abstract
DNA19, Tempe, AZ, Sept, 22-27, 2013. Submitted for journal publication,
(2012). [PDF]
250. John
H. Reif and Wadee Alhalabi, Advancing Attention Control
Using VR-Induced Artificial Synesthesia, submitted
for journal publication, (2018). [PDF]
251. John
H. Reif and Wadee Alhalabi, Design and Analysis of a
High-Efficiency, Cost-Effective Solar Concentrator, submitted
for journal publication, (2014). [PDF]
252. John H.
Reif and Wadee Alhalabi, Solar-Powered Desalination: Its Significant
Challenges and Potential, Renewable and Sustainable Energy Reviews,
Volume 48, Pages 152-165, (August 2015). [PDF] [PDF]
253. Hiba
Shahid, Wadee Alhalabi, and John H. Reif, Real-time operating system (RTOS)
with application to play models, International Journal of Computing Engineering
Research, Vol.5(2), pp. 9-16, October 2014, DOI: 10.5897/IJCER2013.0202, ISSN:
2141-6494, (Oct, 2014). [PDF]
254. Wadee
Alhalabi, John Reif, Zeineb Elsheikh, Heba Felimban, Majda Fallata, Khalid
Thabit, Abdullah Abusorrah, The Co-learning in the Design,
Simulation and Optimization of a Solar Concentrating System, Computers in Human
Behavior, Vol 51, Part B, pp. 857-866 (December 2014). [PDF] https://dx.doi.org/10.1016/j.chb.2014.10.043
255. Tianqi
Song, Sudhanshu Garg, Hieu Bui, Reem Mokhtar, and John H. Reif, Analog
Computation by DNA Strand Displacement Circuits, ACS Synthetic
Biology, 5, 898−912 (July, 2016). DOI:
10.1021/acssynbio.6b00144 [PDF] [PDF]
256. Hieu Bui,
Sudhanshu Garg, Vincent Miao, Tianqi Song, Reem Mokhtar, and John
Reif, Design and Analysis of Linear Cascade DNA Hybridization Chain Reactions
Using DNA Hairpins, Special Issue, Journal of New Physics,
Vol. 19, (2017) 015006. doi:10.1088/1367-2630/aa53d0 [PDF] [PDF].
257. Sudhanshu
Garg, Shalin Shah, Hieu Bui, Tianqi Song, Reem Mokhtar, and John Reif,
Renewable Time‐Responsive DNA Circuits, Small 14, 1801470(July 18,
2018). [PDF] [PDF] DOI:
10.1002/smll.201801470 https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201801470
258.
Hieu Bui, Shalin Shah, Reem Mokhtar, Tianqi Song, Sudhanshu Garg, John
Reif, Localized
DNA Hybridization Chain Reactions on DNA Origami, ACS Nano, Volume 12, Num. 2, pp 1146–1155(January 22, 2018). DOI: 10.1021/acsnano.7b06699
259. Daniel Daniel
Fu, Shalin Shah, Tianqi Song and John H Reif, DNA-based Analog
Computing, Chapter in book: Synthetic Biology: Methods and
Protocols, Edited by Jeffrey C. Braman), In Series Methods in Molecular
Biology, published by Springer, pp. 411-417 (2018). ISBN
978-1-4939-7795-6 [PDF] [PDF]
260. Tianqi
Song, Sudhanshu Garg, Hieu Bui, Reem Mokhtar, and John
H Reif, Design
and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation
Using Autocatalytic Amplifiers, ACS Synthetic Biology
(Dec 2017). DOI: 10.1021/acssynbio.6b00390
261. Xin
Song, Abeer Eshra, Chris Dwyer, and John Reif, Renewable
DNA Seesaw Logic Circuits Enabled by Photoregulation of Toehold-Mediated Strand
Displacement, RSC Advances, Volume 7, Issue 45, pp.
28130-28144 (March, 2017). DOI: 10.1039/C7RA02607B [PDF] (supplementary: [PDF])
262. Sudhanshu Garg, Hieu Bui, Abeer Eshra, Shalin
Shah and John H Reif, Nucleic Acid Hairpins: A Robust and Powerful
Motif for Molecular Devices, Chapter 7 in book: “Soft Nanomaterials” (Edited
by Ye Zhang and Bing Xu), World Scientific Series in Nanoscience and Nanotechnology,
World Scientific, Volume 19,
pp. 175-199 (2019). ISBN: 978-981-120-102-8, DOI:
10.1142/9789811201035_0007
263. John H.
Reif, DNA
robots sort as they walk, Prospective, Science, Vol. 357, Issue 6356,
pp. 1095-1096 (September, 2017). DOI: 10.1126/science.aao5125
264. Hieu Bui and John H Reif, Localized DNA Computation,
Chapter 19 in book: “From Parallel to Emergent Computing” (Edited by Andrew Adamatzky, Selim Akl, and Georgios Ch. Sirakoulis), CRC Press (February 18, 2019). Taylor
& Francis Group of CRC Press. ISBN:
9781138054011
265. Shalin Shah and John
H. Reif, Temporal DNA Barcodes: A Time-Based Approach for Single-Molecule
Imaging, 24th International Conference, DNA 24, Jinan, China, Also, Chapter 5
of DNA Computing and Molecular Programming (DNA 2018), edited by D. Doty
and H. Dietz, LNCS 11145, published by Springer Nature Switzerland
AG, pp.71-86, (2018). DOI: 10.1007/978-3-030-00030-1_5 Also
published as Shah, Shalin, Abhishek Dubey, and John Reif. "Improved
optical multiplexing with temporal DNA barcodes." ACS Synthetic Biology
8.5 (2019): 1100-1111. DOI: 10.1021/acssynbio.9b00010
266. Tianqi Song, Nikhil Gopalkrishnan, Abeer Eshra,
Sudhanshu Garg, Reem Mokhtar, Hieu Bui, Harish Chandran and John Reif,
Improving the Performance of DNA Strand Displacement Circuits by Shadow
Cancellation, ACS Nano, (Oct 29, 2018). DOI: 10.1021/acsnano.8b07394 https://doi.org/10.1021/acsnano.8b07394
267. Abeer
Eshra, Shalin Shah, Tianqi Song, John Reif, Renewable
DNA hairpin-based logic circuits, IEEE Transactions on Nanotechnology, Vol. 18,
pp. 252-259, (2019). DOI: 10.1109/TNANO.2019.2896189
268. Shalin
Shah, Dubey Abhishek and John H. Reif, Programming
temporal DNA barcodes for single-molecule fingerprinting, Nano
letters, 19 (4), pp 2668–2673 (March 2019). DOI: 10.1021/acs.nanolett.9b00590
269. Xin
Song and John H Reif, Nucleic Acid Databases and Molecular-Scale
Computing, ACS Nano, Vol 13, Issue 6, pp 6256-6268 (May
2019). DOI: 10.1021/acsnano.9b02562
270. 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
271. 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). DOI: 10.1021/jacs.9b05598 https://doi.org/10.1021/jacs.9b05598
272. Shalin Shah., Tianqi Song, Xin Song, Ming Yang, John H. Reif,
Implementing Arbitrary CRNs Using Strand Displacing Polymerase. In: Thachuk C.,
Liu Y. (eds) DNA Computing and Molecular Programming. International
Conference on DNA Computing and Molecular Programming (DNA
2019). Lecture Notes in Computer Science, vol 11648. Springer, Cham, pp 21-36 (2019).
DOI:
10.1007/978-3-030-26807-7_2. Published as Chapter in: DNA Computing and Molecular
Programming (edited by Chris Thachuk and Yan Liu), Volume 11648, Springer,
Switzerland AG, pp 21-36, (2019). ISBN: 978-3-030-26807-7. [PDF]
273. Xin Song, Shalin Shah, and John Reif, An Overview of DNA-Based Digital
Data Storage, Chapter 18, DNA- and RNA-Based Computing Systems (Evgeny Katz,
editor), Wiley-VCH Verlag GmbH Publishers, Weinheim, Germany, pp. 345-350
(Dec., 2020). ISBN: 978-3-527-82541-7
274. Reem Mokhtar, Tianqi
Song, Daniel Fu, Shalin Shah, Xin Song, Ming Yang, and John Reif, DNA Origami
Transformers, Chapter 16, DNA- and RNA-Based Computing Systems (Evgeny Katz,
editor), Wiley-VCH Verlag GmbH Publishers, Weinheim, Germany, pp. 307-322
(Dec., 2020). ISBN: 978-3-527-82541-7 [PDF]
275. Xin Song, Daniel Fu,
Shalin Shah, John Reif, UV-Micropatterned
Miniaturization: Rapid In-Situ Photopatterning and Miniaturization of
Microscale Features on Shrinkable Thermoplastics, Advanced Materials, Vol. 5,
Issue 6 (May 4,2020). DOI: 10.1002/admt.202000146 https://doi.org/10.1002/admt.202000146
276. Shalin Shah, Jasmine Wee, Tianqi Song, Luis Ceze, Karin
Strauss, Yuan-Jyue Chen, John Reif, Using strand displacing polymerase to
program chemical reaction networks, Journal of the American Chemical Society
(JACS), Vol. 142, Issue. 21, pp. 9587–9593 (May 4, 2020). DOI:
10.1021/jacs.0c02240 https://pubs.acs.org/doi/10.1021/jacs.0c02240
(Supporting Information https://pubs.acs.org/doi/10.1021/jacs.0c02240).
277. Xin Song and John Reif, Optics-Free Imaging with DNA
Microscopy: An Overview, Chapter 6. Handbook of Unconventional Computing:
Volume 2: Implementations (edited by Andrew Adamatzky), WSPC Book Series in
Unconventional Computing, World Scientific Publishers (WSPC), pp. 181-191
(2021). DOI: 10.1142/12232 DOI: 10.1142/9789811235740_0006. [PDF] ISBN:
978-981-123-527-6 (ebook), 978-981-123-503-0 (hardcover).
278. Shalin Shah, Ming Yang, Tianqi Song, and John Reif,
Molecular computation via polymerase strand displacement reactions, Chapter 5.
Handbook of Unconventional Computing: Volume 2: Implementations (edited by
Andrew Adamatzky), WSPC Book Series in Unconventional Computing, World
Scientific Publishers, pp. 165-197 (2021) [PDF] DOI:
10.1142/9789811235740_0005. ISBN: 978-981-123-527-6 (ebook), 978-981-123-503-0
(hardcover).
279. Daniel Fu, Raghu
Narayanan Pradeep, Fei Zhang, John Schreck, Hao Yan and John Reif, Automated
Design of Curved DNA Origami Nano-Capsules with Specific Shape and Variable
Multilayer-Reinforced Rigidity, International Conference on DNA Computing and Molecular
Programming (DNA 2019), Seattle, WA (Aug, 2019).
281. Daniel Fu and John H Reif, 3D DNA Nanostructures: The
Nanoscale Architect. special issue (Mechanical Design in DNA Nanotechnology)
of Applied Sciences, Volume 11, No. 6, eLocator-ID 2624, (2021). DIO: https://doi.org/10.3390/app11062624
282. Xin Song, Shalin Shah, John Reif,
Multidimensional Data Organization and Random Access in Large-Scale DNA Storage
Systems, special issue of Natural Computing (Theoretical Computer Science –
track C), Vol. 894, pp. 190–202 (2021). DIO:
https://doi.org/10.1016/j.tcs.2021.09.021
283. Xin Song, Felicity Coulter, Ming Yang,
Fikadu Tafesse, William Messer, John Reif, Lyophilized Colorimetric RT-LAMP Test Kit for Rapid, Low-Cost, At-Home Molecular Testing of
SARS-CoV-2 and Other Pathogens, Scientific Reports,12: 7043 (April 2022). DOI: 10.1038/s41598-022-11144-5.
284. Ming Yang, and John H. Reif, Social DNA Nanorobots, pp 371-396, Invited Chapter for Book on
DNA Nanotechnology at 40 for the next 40 - A Tribute to Nadrian C. Seeman,
(edited by Natasha Jonoska and Erik Winfree, book series Natural Computing,
Springer (2023).
285. Daniel Fu, Raghu Pradeep Narayanan, Abhay
Prasad, Fei Zhang, Dewight Williams, John S. Schreck, Hao Yan, John Reif, Automated
Design of 3D DNA Origami with Non-Rasterized 2D Curvature, Science Advances, Volume
8, Issue 51, (2022). DOI: 10.1126/sciadv.ade4455
286. Rajiv Teja Nagipogu Daniel Fu and John Reif,
Molecular scale learning using DNA circuits” Nanoscale (2022). A survey on molecular-scale learning systems with
relevance to DNA computing, Nanoscale, Royal Society of Chemistry (2023), DOI: 10.1039/d2nr06202j
287. Daniel Fu and John Reif, A Biomimetic
Branching Signal-Passing Tiling Model with Dynamic Assembly and Disassembly. Submitted
for publication, Dec 2023.
288. Rajiv Teja Nagipogu and John H. Reif,
Leak-resilient Nucleic Acid Dynamical Systems through Shadow Cancellation. Submitted
for publication, Dec 2023.
289. Grayson York and John Reif, Nondeterministic
Temperature 1 Self Assembly in 2 Dimensions is Undecidable. Submitted for
publication, Dec 2023.