**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.

**Office phone:** **home
phone:**

(919)
660-6568 (919)
493-7978

**Email address:**

**Reif DNA Nanoscience
Lab: Room 3245, French Family Science Center**

**Homepage:** http://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.

**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)**

Xin Song,
Tentative Ph.D. thesis topic: “Reusable DNA Circuits”. Projected
Date of Graduation: Fall 2021.

Dan Fu,
Tentative Ph.D. thesis topic: “3D DNA Shapes for Nanocasting”.
Projected Date of Graduation: Fall 2021.

Ming
Yang: PhD candidate. Projected Date of Graduation: Spring 2022.

**Graduate Student
Supervision (Completed Degrees):**

Shalin
Shah, Tentative Ph.D. thesis topic: “Families of DNA
Devices for Super-Resolution Imaging”. Date of Graduation: Spring 2020.

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.)

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.)

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
priz) "Stacktracking: Parallel Acceptance of Deterministic Context-Free
Languages", 1984 (Currently Full Professor, Brown University).

**Research Support: Principal
Investigator or Co-Investigator**

NSF CCF-1909848, SHF:
Small: Distributed DNA Computations Operating on a Collection of Cell Membranes
Polymerase (PI John H. Reif), 8/05/2019-08/4/2022, $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. http://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].

6. John H
Reif and Karl F. Bohringer, Microelectronic Devices for Harvesting Vibrational
Energy and Associated Systems and Methods, US Provisional Patent
Application 61/656,425, filed June 6, 2012. US Non-Provisional Patent
Application 13/910,9795, Filed June 5, 2013 [GooglePatent][USPO]. Assignee:
Ruamoko MEMS, 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.

- Member of Advisory Board, Series
on Natural Computing, Springer-Verlag, 2006 - current.
- Member of Advisory Board of Wiley
Book Series on Nature Inspired Computing, 2009-presen.
- Member of Advisory
Board, Springer Series in Computer Science and Computer Security
for Higher Education Press of Ministry of Education of China, 2009 -
current.
- Member of Editorial Advisory
Board, DNA and RNA Nanotechnology, 2014 – current.
- Member of Advisory Board, World
Scientific Series in Unconventional Computing, 2020 – 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, 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)

- John H. Reif, Combinatorial
Aspects of Symbolic Program Analysis. Ph.D. Thesis, Harvard University,
July 1977. [PDF] (Preface & Introductory
Chapter 1:[PDF], Chapter 2(pub. #3):[PDF], Chapter 3:[PDF], Chapter 4(pub. #5):[PDF],Chapter 5(pub. #4):[PDF])
- Richard Barakat and John H. Reif,
Numerical Solution of the Fokker-Plank Equation via Chebyschev
Approximations with Reference to First Passage Time Probability
Functions.
*Journal of Computational Physics*, Vol. 23, No. 4, April 1977, pp. 425-445. [PDF] - John H. Reif and Harry R. Lewis,
Symbolic Evaluation and the Global Value Graph.
*4th ACM Symposium on Principals of Programming Languages*,*Journal of Computer and System Sciences*, - John H. Reif, Code Motion.
Presented at
*Conference on Theoretical Computer Science*,*SIAM Journal on Computing*, Vol. 9, No. 2, May 1980, pp. 375-395. [PDF] - John H. Reif, Symbolic Program
Analysis in Almost Linear Time.
*5th Annual ACM Symposium on Principals of Programming Languages*, Tucson, AZ, January 1978, pp. 76-83. [PDF] Published as John H. Reif and R.E. Tarjan,*SIAM Journal on Computing*, Vol. 11, No. 1, February 1982, pp. 81-93. [PDF] - John H. Reif, Data Flow Analysis
of Communicating Processes.
*6th Annual ACM Symposium on Principals of Programming Languages*,*International Journal of Parallel Programming*, Vol. 19, No. 1, February 1990. [PDF] - John H. Reif, The Complexity of
Extending a Graph Imbedding. Computer Science Department, University of
Rochester, TR-42, October 1978. [PDF]
- Ion S. Filotti, Gary
Miller, and John H. Reif, On Determining the Genus of a Graph in 0(v^0(g))
Steps,
*11th Annual ACM Symposium on Theory of Computing(STOC79)*, Atlanta, GA, April 1979, pp. 27-37. [PDF] - John H. Reif, Universal Games of
Incomplete Information.
*11th Annual ACM Symposium on Theory of Computing*, Atlanta, GA, April 1979, pp. 288-308. Harvard University TR-35-81. [PDF] Published as The Complexity of Two-Player Games of Incomplete Information.*Journal of Computer and System Sciences*, Vol. 29, No. 2, October 1984, pp. 274-301. [PDF]

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]

- John H. Reif, Complexity of the
Mover's Problem and Generalizations.
*20th Annual IEEE Symposium on Foundations of Computer Science*, San Juan, Puerto Rico, October 1979, pp. 421-427. [PDF] Published as Complexity of the Generalized Mover's Problem, Chapter 11 in*Planning, Geometry and Complexity of Robot Motion*, Jacob Schwartz, ed., Ablex Pub., Norwood, NJ, 1987, pp. 267-281. [PDF] - Gary L. Peterson and John H. Reif,
A Dynamic Logic of Multiprocessing with Incomplete Information.
*7th Annual ACM Symposium on Principles of Programming Languages*, - John H. Reif, Logics for
Probabilistic Programming.
*12th Annual ACM Symposium on Theory of Computing*, - John H. Reif and Paul G. Spirakis,
Random Matroids.
*12th Annual ACM Symposium on Theory of Computing*, - John H. Reif and Paul G. Spirakis,
Distributed Algorithms for Synchronizing Interprocess Communication Within
Real Time.
*13th Annual ACM Symposium on Theory of Computing*,*ACM Journal of Transactions on Programming Languages and Systems*, Vol. 6, No. 2, April 1984, pp. 215-238. [PDF] - John H. Reif, Minimum s-t Cut of
Planar Undirected Network in 0(n log^2n) Time, 8th Colloquium on Automata,
Languages and Programming, (Shimon Even and Oded Kariv, editors) volume
115 of Lecture Notes in Computer Science, pp. 56-67, Acre (Akko), Israel,
13-17 July 1981. Springer-Verlag. Published in
*SIAM Journal on Computing*, Vol. 12, No. 1, February 1983, pp. 71-81. [PDF] - John H. Reif, Symmetric
Complementation.
*14th Annual ACM Symposium on Theory of Computing*,*Probabilistic Computational Complexity*,*Journal of the ACM(JACM)*, - Joseph Y. Halpern and John H. Reif,
The Propositional Dynamic Logic of Deterministic, Well-Structured
Programs,
*22nd Annual IEEE Symposium on Foundations of Computer Science*,*Journal of Theoretical Computer Science*, - John H. Reif and Paul G. Spirakis,
Unbounded Speed Variability in Distributed Communication Systems.
*9th Annual ACM Symposium on Principals of Programming Languages(POPL80)*,*SIAM Journal on Computing*, - Gary L. Peterson and John H. Reif,
Decision Algorithms for Multiplayer Games of Incomplete Information.
Harvard University, TR-34-81. Published as Gary L. Peterson, John H. Reif,
and Selman Azhar, Decision Algorithms for Multiplayer Non-Cooperative
Games of Incomplete Information. Computers and Mathematics with
Applications, Vol. 43, Jan. 2002, pp. 179-206. [PDF]
- John H. Reif and Paul G. Spirakis,
K-connectivity in Random Undirected Graphs,
*Discrete Mathematics*, - John H. Reif and Paul G. Spirakis,
Strong k-connectivity in Digraphs and Random Digraphs, Harvard University
TR-25-81. [PDF]
- John H. Reif, On the Power of
Probabilistic Choice in Synchronous Parallel Machines. Harvard University
TR-30-81.
*9th International Colloquium on Automata, Languages and Programming*,*SIAM Journal on Computing*, Vol. 13, No. 1, February 1984, pp. 46-56. [PDF] - John H. Reif and Paul G. Spirakis,
Real Time Resource Allocation in Distributed Systems,
*ACM Symposium on Principals of Distributed Computing*, - John H. Reif, Parallel Time
*0*(log*n*) Time Acceptance of Deterministic CFLs.*23rd Annual IEEE Symposium on Foundations of Computer Science*,*0*(log*n*) Time Acceptance of Deterministic CFLs on an Exclusive-Write P-RAM,*SIAM Journal on Computing*, - John H. Reif and Paul G. Spirakis,
Expected Parallel Time and Sequential Space Complexity of Graph and
Digraph Problems,
*Algorithmica*, Special Issue on Graph Algorithms, Vol. 7, Numbers 5 & 7, pp. 597-630, 1992. [PDF] - Leslie G. Valiant and John H.
Reif, A Logarithmic Time Sort for Linear Size Networks.
*15th Annual ACM Symposium on Theory of Computing*,*Journal of the ACM(JACM)*, - John H. Reif and W.L. Scherlis,
Deriving Efficient Graph Algorithms. Logics of Programs Workshop,
Carnegie-Mellon University, Pittsburgh, PA, June 1983, Lecture Notes in
Computer Science, Vol. 164, 1984, pp. 421-441. Published in: Verification:
Theory and Practice: Essays Dedicated to Zohar Manna on the Occasion of
His 64th Birthday (edited by Nachum Dershowitz), LNCS series Vol. 2772,
pp. 645-681, 2004. [PDF] or [PDF]
- John H. Reif and A.P. Sistla, A
Multiprocess Network Logic with Temporal and Spatial Modalities,
*10th International Colloquium on Automata, Languages and Programming*, Barcelona, Spain, July 1983;*Lecture Notes in Computer Science*, Vol. 154, 1983, pp. 629-639. Published in*Journal of Computer and System Sciences*, - John H. Reif, Logarithmic Depth
Circuits for Algebraic Functions.
*24th Annual IEEE Symposium on Foundations of Computer Science*, Tucson, AZ, November 1983, pp. 138-145. Published in*SIAM Journal on Computing*, - John H. Reif, An
n1+epsilon Processor, 0(log n) Time Probabilistic Sorting
Algorithm.
*SIAM 2nd Conference on the Applications of Discrete Mathematics*, - John H. Reif, Probabilistic
Parallel Prefix Computation,
*13th Annual International Conference on Parallel Processing*,*Computers and Mathematics with Applications*, Vol. 26, Number 1, July 1993, pp. 101-110. [PDF] - John H. Reif and Paul G. Spirakis,
Probabilistic Bidding Gives Optimal Distributed Resource Allocation.
*11th International Colloquium on Automata, Languages and Programming*,*Lecture Notes in Computer Science*, Vol. 172, pp. 391-402. [PDF] - John H. Reif, Depth-First Search
is Inherently Sequential.
*Information Processing Letters*, - John H. Reif, A Topological
Approach to Dynamic Graph Connectivity.
*Information Processing Letters*, - Gautam Kar, Christos N. Nikolaou,
and John H. Reif, Assigning Processes to Processors: A Fault-Tolerant
Approach,
*14th International Conference on Fault-Tolerant Computing*, - Micheal Ben-Or, Dextor Kozen, and
John H. Reif, The Complexity of Elementary Algebra and Geometry.
*16th Annual Symposium on Theory of Computing*, Washington, DC, April-May 1984,*Journal of Computer and Systems Sciences*, - Ravi Nair, Anni Bruss, and John H.
Reif, Linear Time Algorithms for Optimal CMOS Layout,
*International Workshop on Parallel Computing and VLSI*, Amalfi, Italy, May 1984;*VLSI: Algorithms and Architectures*, - John H. Reif and Doug Tygar,
Efficient Parallel Pseudo-random Number Generation.
*CRYPTO-85, Proceedings*, Vol. 218, H. Williams and E. Brickell, ed., Springer-Verlag, New York, NY, 1986, pp. 433-446 Presented at the Mathematical Theory of Security, Boston, MA, 1985. Published in*SIAM Journal on Computing*, Vol. 17, No. 2, April 1988, pp. 404-411. [PDF] - Peter Gacs and John H. Reif, A
Simple Three-dimensional Real-time Reliable Cellular Array.
*17th Annual ACM Symposium on Theory of Computing*, Providence, RI, May 1985, pp. 388-395. [PDF] Published in*Journal of Computer and System Sciences*, - Victor Y. Pan and John H. Reif,
Efficient Parallel Solution of Linear Systems.
*17th Annual ACM Symposium on Theory of Computing(STOC85)*, Providence, RI, (ACM Press, New York) May 1985,*2nd SIAM Conference on Applied Linear Algebra*, Raleigh, NC, April 1985. Published as Fast and Efficient Parallel Solution of Sparse Linear Systems.*SIAM Journal on Computing*, Vol 22, No. 6, pp. 1227-1250, December 1993. [PDF] or [PDF] - Gary Miller and John H. Reif,
Parallel Tree Contraction and its Application. Harvard University
TR-18-85.
*26th Annual IEEE Symposium on Foundations of Computer Science*, Portland, OR, October 1985, pp. 478-489.

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]

- Sanguthevar Rajasekaran and John
H. Reif, An Optimal Parallel Algorithm for Integer Sorting.
*26th Annual IEEE Symposium on Foundations of Computer Science*, Portland, OR, October 1985,*SIAM Journal on Computing*, Vol. 18, No. 3, June 1989, pp. 594-607. [PDF] or [PostScript] [PDF] - John H. Reif and M. Sharir, Motion
Planning in the Presence of Moving Obstacles,
*26th Annual IEEE Symposium on Foundations of Computer Science*, Portland, OR, October 1985,*JACM)*, 41:4, July 1994, pp. 764-790. [PDF] or [PostScript] [PDF] - John H. Reif, Probabilistic
Algorithms in Group Theory. Foundations of Computation Theory (FCT85),
Cottbus, Democratic Republic of Germany, September 1985;
*Lecture Notes in Computer Science*, Vol. 199, 1985, pp. 341-350. Also TR85-01, Dept. of Computer Science, Harvard University, (1985). Published as Selman Azhar and John H. Reif, Efficient Algorithmic Learning of the Structure of Permutation Groups by Examples,*Computers & Mathematics with Applications*, Volume 37, Issue 10, May 1999, pp. 105-132. [PDF] - Victor Y. Pan and John H. Reif,
Fast and Efficient Algorithms for Linear Programming and for the Linear
Least Squares Problem,
*12th International Symposium on Mathematical Programming*,*Operations Research Letters*,*Lecture Notes in Computer Science*, Springer-Verlag, Vol. 227, 1986, pp. 283-295. Full Paper published as Fast and Efficient Linear Programming and Linear Least-Squares Computations,*Computers and Mathematics with Applications*, - John H. Reif, Parallel
Interpolation Search.
*23rd Annual Allerton Conference on Communication, Control and Computing*,*Journal of Information and Computation*, Vol. 81, No. 3, June 1989, pp. 364-379. [PDF] - John H. Reif and Scott A. Smolka,
The Complexity of Reachability in Distributed Communicating
Processes,
*Journal of Acta Informatica*, - Steve Homer and John H. Reif,
Arithmetic Theories for Computational Complexity Problems,
*Journal of Information and Control*, Vol. 69, nos. 1-3, April/May/June 1986, pp. 1-11. [PDF] - James A. Storer and John H. Reif,
A Parallel Architecture for High Speed Data Compression,
*3rd Symposium on the Frontiers of Massively Parallel Computation*, College Park, MD, October 1990, pp. 238-243. Published in Journal of Parallel and Distributed Computation, No. 13, 1991, pp. 222-227. [PDF] - Victor Y. Pan and John H. Reif,
Fast and Efficient Parallel Solution of Dense Linear Systems.
*Computers and Mathematics with Applications*, Vol. 17, No. 11, 1989, pp. 1481-1491. [PDF] - John H. Reif and James A.
Storer, Shortest Paths in the plane with polygonal obstacles,
*Journal of the ACM(JACM)*41:5, September, 1994, pp. 982-1012. [PDF] - John H. Reif and James A. Storer,
Minimizing Turns for Discrete Movement in the Interior of a Polygon,
*IEEE Journal of Robotics and Automation*, - John H. Reif, Efficient VLSI Fault
Simulation.
*Computers and Mathematics with Applications*, Vol 25, No. 2, Jan. 1993, pp. 15-32. [PDF] - Richard E. Ladner and John H.
Reif, The Logic of Distributed Protocols.
*Conference on Theoretical Aspects of Reasoning about Knowledge*, Los Altos, CA, March 1986, pp. 207-223. [PDF] - Victor Y. Pan and John H. Reif, Extension
of the Parallel Nested Dissection Algorithm to Path Algebra Problems.
Presented at
*6th Conference on Foundation of Software Technology and Theoretical Computer Science*,*Lecture Notes in Computer Science*, Springer Verlag, Vol. 241, pp. 470–487, 1986. An abstract of this paper appears as Parallel Nested Dissection for Path Algebra Computations,*Operations Research Letters*,*Journal of Computer and Systems Sciences*, Vol. 38, No. 3, June 1989, pp. 494-510. [PDF] - John
Canny and John H. Reif, New Lower Bound Techniques for Robot Motion
Planning Problems.
*28th Annual IEEE Symposium on Foundations of Computer Science*, - Richard Barakat and John H. Reif,
Lower Bounds on the Computational Efficiency of Optical Computing
Systems.
*Journal of Applied Optics*, - Richard Barakat and John H. Reif,
Polynomial Convolution Algorithm for Matrix Multiplication with
Application for Optical Computing. Published in
*Journal of Applied Optics*, - John H. Reif, A Survey on Advances
in the Theory of Computational Robotics. Proceedings of the Fourth
Workshop of Adaptive Systems Control Theory, Princeton, NJ, 1986. Also as
Chapter in Book: Adaptive and Learning Systems: Theory and
Applications, Princeton, NJ
*(edited by*K.S. Narendra), Plenum Press, New York, NY, pp. 421--427 1986. [PDF] - Phlip Klein and John H. Reif, An
Efficient Parallel Algorithm for Planarity.
*27th Annual IEEE Symposium on Foundations of Computer Science*, Toronto, Canada, October 1986,*Journal of Computer and System Sciences*, - Charles E. Leiserson, J.P.
Mesirov, L. Nekludova, S.M. Omohundro, John H. Reif, and W. Taylor,
Solving Sparse Systems of Linear Equations on the Connection
Machine.
*Annual SIAM Conference*, Boston, MA, July 1986. [PDF] - T. Opsahl and John H. Reif,
Solving Very Large, Sparse Linear Systems on Mesh-Connected Parallel
Computers.
*First Symposium on Frontiers of Scientific Computing*, - John H. Reif, Simon Kasif,
and Deepak Sherlekar, Formula Dissection: A Parallel Algorithm
for Constraint Satisfaction.
*IEEE Workshop on Computer Architecture for Pattern Analysis and Machine Intelligence*, Seattle, WA, October 1987, pp. 51-58. Published in Computers and Mathematics with Applications, Vol. 5, (2008), pp. 1170-1177. [PDF] [PDF] - John H. Reif and Sandeep Sen,
Optimal Randomized Parallel Algorithms for Computational Geometry.
*16th International Conference on Parallel Processing*, St. Charles, IL, August 1987, pp. 270-276. Published in*Algorithmica*, Vol. 7, No. 1, January 1992, pp. 91-117. [PDF] - John Canny, B. Donald, John H.
Reif and Patrick G. Xavier. On the Complexity of Kinodynamic Planning.
*29th Annual IEEE Symposium on Foundations of Computer Science*,*Journal of the ACM*, Vol 40(5), November 1993, pp. 1048-1066. [PDF] - Sanguthevar Rajasekaran and John
H. Reif, Randomized Parallel Computation. Presented at
*Foundations of Computation Theory Conference*,*Lecture Notes in Computer Science*,*Concurrent Computations: Algorithms, Architecture and Technology*, - John H. Reif and Steve R. Tate, On
Threshold Circuits and Polynomial Computation.
*2nd Structure in Complexity Theory Conference*,*SIAM Journal on Computing*, Vol.21, No. 5, October 1992, 896-908. [PDF] or [PostScript] [PDF] - Vijaya Ramachandran and John
H. Reif, An Optimal Parallel Algorithm for Graph Planarity.
*30th Annual IEEE Symposium on Foundations of Computer Science*, Research Triangle Park, NC, October 1989, pp. 282-287. Published as Planarity Testing in Parallel*, Journal of Computer and System Sciences*,**49**:3, December, 1994, pp. 517-561. [PostScript] [PDF] - Sanguthevar Rajasekaran and John
H. Reif, Nested Annealing: A Provable Improvement to Simulated Annealing.
Presented at
*Workshop on Applications of Combinatorics and Graph Theory to Computer Science*, Institute for Mathematics and its Applications, University of Minnesota, December 1987. Presented at the*15th International Colloquium on Automata, Languages and Programming*,*Lecture Notes in Computer Science*, Vol. 317, 1988, pp. 455-472. Published in*Journal of Theoretical Computer Science*, 99(1):157-176, 1 June 1992. [PDF] - Victor Y. Pan and John H. Reif,
Some Polynomial and Toeplitz Matrix Computations.
*28th Annual IEEE Symposium on Foundations of Computer Science*, Los Angeles, CA, October 1987, (IEEE Computer Society Press) - James A. Storer and John H. Reif,
Real-time Compression of Video on a Grid-connected Parallel
Computer.
*3rd International Conference on Supercomputing*, - Edward W. Davis and John H. Reif,
Architecture and Operation of the BLITZEN Processing Element.
*3rd International Conference on Computing on Supercomputing*, - John H. Reif and Sandeep Sen, An
Efficient Output-Sensitive Hidden-Surface Removal Algorithm and its
Parallelization.
*4th Annual ACM Symposium on Computational Geometry*,*Journal of Mathematical and Computer Modeling*, Vol. 21, No. 5, pp. 89-104, 1995. [PDF] or [PDF] - Lars S. Nyland and John H. Reif,
An Algebraic Technique for Generating Optimal CMOS Circuitry in Linear
Time,
*Computers and Mathematics with Applications*Vol 31, No. 1, Jan. 1996, pp.85-108. [PDF] - Donald W. Blevins, Edward W.
Davis, Richard A. Heaton and John H. Reif, BLITZEN: A Highly Integrated
Massively Parallel Machine.
*2nd Symposium on Frontiers of Massively Parallel Computation*,*Journal of Parallel and Distributed Computing*, Vol. 8, February 1990, pp. 150-160. [PDF] - John H. Reif and Steve R. Tate,
Optimal Size Integer Division Circuits.
*21st Annual ACM Symposium on Theory of Computing*, Seattle, WA, May 1989,*SIAM Journal on Computing*, Vol. 19, No. 5, October 1990, pp. 912-924. [PDF] or [PostScript] [PDF] or [PostScript] - John H. Reif and Sandeep Sen,
Polling: A New Randomized Sampling Technique for Computational
Geometry,
*21st Annual ACM Symposium on Theory of Computing*, Seattle, WA, May 1989, pp. 394-404. [PDF] Revised as Optimal Parallel Randomized Algorithms for Three-Dimensional Convex Hulls and Related Problems, Published in*SIAM Journal on Computing*, Vol. 21, No. 3, June 1992, pp. 466-485. [PDF] or [PDF] (see also Erratum: Optimal parallel randomized algorithms for three-dimensional convex hulls and related problems. SIAM Journal on Computing, 23(2):447-448, April 1994. [PDF]) - John H. Reif and A. Tyagi, Energy
Complexity of Optical Computations,
*2nd IEEE Symposium on Parallel and Distributed Processing*, Dallas, TX, December 1990, pp. 14-21. Revised for Journal Publication in International Journal of Unconventional Computing, 2016, Vol. 12 Issue 5/6, pp. 393-412. [PDF] [PDF] - John H. Reif, Optical expanders
give constant time holographic routing using O(N log N) switches, 1988 [PDF]. Full paper appeared as E.S.
Maniloff, K. Johnson, and John H. Reif, Holographic Routing Network for
Parallel Processing Machines
*Holographic Optics II: Principals and Applications*, G. Michael Morris; Ed. - John H. Reif, Doug Tygar, and
Akitoshi Yoshida, The Computability and Complexity of Optical Beam
Tracing.
*31st Annual IEEE Symposium on Foundations of Computer Science*, St. Louis, MO, October 1990, pp. 106-114. Published as The Computability and Complexity of Ray Tracing in*Discrete & Computational Geometry*, 11: pp. 265-287 (December 1994). [PDF] - Selman Azhar, Andrew McLennan and
John H. Reif, Computation of Equilibria in Noncooperative Games, Duke
University Technical Report CS-1991-36.
*Proc. Workshop for Computable Economics*, Dec. 1992. Published in Computers & Mathematics with Applications, Volume 50, Issues 5-6, September 2005, pp. 823-854. [PDF] - R. Paturi, Sanguthevar
Rajasekaran, and John H. Reif, Efficient and Robust Learning Using
Statistical Bootstrap,
*Proceedings of the 2nd Annual Workshop on Computational Learning Theory*, Santa Cruz, CA, August 1989. [PostScript] [PDF] Published as The Light Bulb Problem,*Information and Computation*, 117(2):187-192, March 1995. [PDF] - John H. Reif and Sandeep Sen,
Randomized Parallel Algorithms.
*IBM Workshop on Capabilities and Limitations of Parallel Computing*, San Jose, CA, December 1988.*Information Processing**89*, G. Ritter, ed., Elsevier Science Publishers, North Holland, 1989, pp. 455-458. [PDF] A Case for Randomized Parallel Algorithms in*Opportunities and Constraints of Parallel Computing*, J.L.C. Sanz (ed.), Springer-Verlag New York, 1989, pp. 101-105. Also presented as Randomization in Parallel Algorithms and its Impact on Computational Geometry, in*Optimal Algorithms*;*Lecture Notes in Computer Science*, Vol. 401, 1989, pp. 1-8. [PDF] Also presented as C. Pandurangan, Sanguthevar Rajasekaran, John H. Reif, Sandeep Sen, Studies on Sequential and Parallel Randomized Algorithms, Indo-US Workshop on Cooperative Research in Computer Science, Bangalore, India, August 4-6, 1992. [PDF] - Victor Y. Pan and John H. Reif, On
the Bit-Complexity of Discrete Approximations to PDEs.
*International Colloquium on Automata, Languages, and Programming(ICALP 90)*, Warwich, England, Springer Lecture Notes in Computer Science 443, pp. 612-625, July 1990. [PDF] Published as The Bit-Complexity of Discrete Solutions of Partial Differential Equations: Compact Multigrid,*Computers and Mathematics with Applications,*Vol. 20, No. 2, 1990, pp. 9-16. [PDF]. - John H. Reif and A. Tyagi,
Efficient Algorithms for Optical Computing with the DFT Primitive,
Presented at
*10th Conference on Foundations of Software Technology and Theoretical Computer Science*, Bangalore, India,*Lecture Notes in Computer Science, pp. 149-160 (*December 1990). Published as Efficient Algorithms for Optical Computing with the discrete Fourier transform (DFT) primitive,*Journal of Applied Optics*, Vol. 36, 1997, pp. 7327-7340. [PDF] or [PostScript] [PDF] - John Canny, A. Rege, and John H.
Reif, An Exact Algorithm for Kinodynamic Planning in the Plane.
*6th Annual ACM Symposium on Computational Geometry*, Berkeley, CA, June 1990, pp. 271-280. [PDF] Published in*Discrete and Computational Geometry*, Vol. 6, 1991, pp. 461-484. [PDF] - John
H. Reif and Sandeep Sen, Randomized Algorithms for Binary Search and Load
Balancing on Fixed Connection Networks with Geometric Applications.
*2nd Annual ACM Symposium on Parallel Algorithms and Architectures*, Crete, Greece, July 1990, pp. 327-337. Published in*SIAM Journal of Computing*23:3, June, 1994, pp.633-651. [PDF] - John H. Reif, Efficient Parallel
Algorithms: Theory and Practice.
*SIAM 35th Anniversary Meeting*, Denver, CO, October 1987.*XI World Computer Congress*, IFIP 89, San Francisco, CA, 1989. - Hristo Djidjev and John H. Reif,
An Efficient Algorithm for the Genus Problem with Explicit Construction of
Forbidden Subgraphs.
*23rd Annual ACM Symposium on Theory of Computing*, New Orleans, LA, May 1991, pp. 337-347. [PDF] - Hillel Gazit and John H. Reif, A
Randomized Parallel Algorithm for Planar Graph Isomorphism.
*2nd Annual ACM Symposium on Parallel Algorithms and Architectures*, Crete, Greece, July 1990, pp. 210-219. Published in*Journal of Algorithms,*Vol. 28, No. 2, pp. 290-314, August 1998. [PostScript] [PDF] - Victor Y. Pan and John H. Reif,
The Parallel Computation of Minimum Cost Paths in Graphs by Stream
Contraction,
*Information Processing Letters*, Vol. 40, October 25,1991, pp. 79-83. [PDF] - John H. Reif and Steve R. Tate,
Approximate Kinodynamic Planning Using
*L*2-norm Dynamic Bounds. Duke University Technical Report CS-1990-13, 1989. Published in*Computers and Mathematics with Applications*, Vol. 27, No.5, pp.29-44, March 1994. [PostScript] [PDF] - Royals, M., Tassos Markas, N.
Kanopoulos, John H. Reif and James A. Storer, On the Design and
Implementation of a Lossless Data Compression and Decompression Chip,
IEEE Journal of Solid State Circuits (JSSC), Vol. 28, No. 9, pp.
948-953, Sep. 1993. [PDF]
- Micheal Karr, S. Krishnan, John H.
Reif, Derivation of the Ellipsoid Algorithm, Duke University Technical
Report CS-1991-17, (1990). [PDF]
- John H. Reif and A. Tyagi, An
Optical Delay Line Memory Model with Efficient Algorithms.
*Advanced Research in VLSI Conference*, MIT Press, Santa Cruz, CA, March 1991. Published in*Optical Engineering*, 36(09), pp. 2521-2535, Sept. (1997). [PostScript] [PDF] - Selman Azhar and John H. Reif,
Crypto-Complexity Based Models of Efficiency in Capital Markets, 1994. [PDF]
- John H. Reif and Steve R. Tate,
Continuous Alternation: The Complexity of Pursuit in Continuous Domains,
Special Issue on Computational Robotics: the Geometric Theory of
Manipulation, Planning and Control,
*Algorithmica*, Vol. 10, pp. 151-181, 1993. [PostScript] [PDF] - John H. Reif and Akitoshi Yoshida,
Optical Expanders with Applications in Optical Computing,
*Journal of Applied Optics*, 32, 1993, pp. 159-165. [PDF] or [PostScript] [PDF] - James A. Storer and John H. Reif,
Low-Cost Prevention of Error Propagation for Data Compression with Dynamic
Dictionaries,
*Proceedings: IEEE Data Compression Conference (DCC'97)*Snowbird, UT, IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), March 1997, pp. 171-180. Published as Error Resilient Optimal Data Compression, SIAM Journal of Computing (SICOMP), Vol 26, Num 4, July 1997, pp. 934-939. [PostScript] [PDF] - Peter H. Mills, Lars S. Nyland,
J.F. Prins, John H. Reif and Robert A. Wagner, Prototyping Parallel and
Distributed Programs in
*Proteus*.*3rd IEEE Symposium on Parallel and Distributed Processing*, Dallas, TX, pp. 10-19, IEEE, 1991. [PostScript] [PDF] - James A. Storer, Tassos Markas and
John H. Reif, A Massively Parallel VLSI Compression System using a Compact
Dictionary.
*IEEE Workshops on VLSI & Signal Processing*, 1990, San Diego, CA. Published as A Massively Parallel VLSI Design for Data Compression Using a Compact Dictionary,*VLSI Signal Processing*, No. 4, 1990 (edited by H.S. Moscovitz and K. Yao and R. Jain), Chapter 32, IEEE Press, 1990, New York, NY, pp. 329-338. [PDF] - S. Krishnan and John H. Reif,
Towards Randomized Strongly Polynomial Algorithms for Linear Programming,
Duke University Technical Report CS-1991-18. [PDF]
- Victor Y. Pan and John H. Reif,
Decreasing the Precision of Linear Algebra Computations by Using Compact
Multigrid and Backward Interval Analysis.
*4th SIAM Conference in Applied Linear Algebra*,*SIAM Journal of Scientific and Statistical Computing*, Vol. 13, No. 1, pp. 119-127, (1992). [PDF] - Tassos Markas and John H. Reif,
Fast Computations of Vector Quantization Algorithms. NASA Technical Report
TR-91-58, 1991.
- Tassos Markas and John H. Reif,
Image Compression Methods with Distortion Controlled Capabilities.
*IEEE Data Compression Conference (DCC 91)*, Snowbird, UT, IEEE Computer Society Press, April 1991, pp. 93-102. Published as Quad Tree Structures for Image Compression Applications, special issue of*Journal of Information Processing and Management*, 1992, pp. 707-721. [PDF] - Joseph Cheriyan and John H. Reif,
Algebraic Methods for Testing the
*k*-Vertex Connectivity of Directed Graphs,*3rd Annual ACM-SIAM Symposium on Discrete Algorithms*, Orlando, Florida,*s-t*Numberings, Rubber Bands, and Testing Digraph*k*-Vertex Connectivity, in*Combinatorica*14(4) pp. 435-451, 1994. [PDF] - John H. Reif and Akitoshi Yoshida,
Optical Techniques for Image Compression.
*2nd Annual IEEE Data Compression Conference (DCC 92)*, Snowbird, UT, IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), March 1992, pp. 32-41. Also in*Image and Text Compression*, edited by James A. Storer, Kluwer Academic Publishers, 1992. Published as "Optical Computing Techniques for Image/Video Compression," in*Proceedings of the IEEE*, 82:6, June 1994, pp. 948-954. [PDF] - John H. Reif and Hongyan Wang, On
Line Navigation Through Regions of Variable Densities. ARO Computational
Geometry Workshop, Raleigh, North Carolina, October, 1993. Rewritten as
On-Line Navigation Through Weighted Regions. [PostScript] [PDF]
- Ming Kao, John H. Reif, and Steve
R. Tate, Searching in an Unknown Environment: An Optimal Randomized
Algorithm for the Cow-Path Problem,
*Proceedings of the**4th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'93),*Austin, TX, Jan 1993, pp.441-447. Published in*Information and Computation, Vol 131, No. 1*(1996), p 63-80. [PostScript] [PDF] - John H. Reif, O(log2 n) Time
Efficient Parallel Factorization of Dense, Sparse Separable, and Banded
Matrices.
*5th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'94)*, Cape May, NJ, June 1994, pp. 114-121. - John H. Reif, An
*O*(*n*log^3*n*) Algorithm for the Real Root Problem.*34th Annual IEEE Conference on Foundations of Computer Science (FOCS '93) Proceedings*, November 1993, Palo Alto, CA, pp. 626-635. Revised as An Efficient Algorithm for the Real Root and Symmetric Tridiagonal Eigenvalue Problems, 1994. [PostScript] [PDF] and [PostscriptFigures] - Tassos Markas and John H. Reif,
Memory-Shared Parallel Architectures for Vector Quantization Algorithms,
1992. Picture Coding Symposium, Lusanne Switzerland, March, 1993.
- Peter H. Mills, Lars S. Nyland,
Jan Prins, and John H. Reif, Prototyping N-body Simulation in
*Proteus*,*Sixth International Parallel Processing Symposium*, IEEE, Beverly Hills, CA, pp. 476-482, 1992. [PostScript] [PDF] - Deganit Armon and John H.
Reif, Space and time efficient implementations of parallel nested
dissection,
*4th Annual ACM Symposium on Parallel Algorithms and Architectures*, San Diego, CA, July 1992. Submitted for journal publication as Space and Time Efficient Implementations of a Parallel Direct Solver using Nested Dissection. [__PDF__] - Peter H. Mills, Lars S. Nyland,
Jan Prins, and John H. Reif, Prototyping High-Performance Parallel
Computing Applications in
*Proteus*.*DARPA Software Technology Conference*, May, 1992. [PostScript] [PDF] - Victor Y. Pan, John H. Reif, Steve
R. Tate. The Power of Combining the Techniques of Algebraic and Numerical
Computing: Improved Approximate Multipoint Polynomial Evaluation and
Improved Multipole Algorithms,
*32th Annual IEEE Symposium on Foundations of Computer Science (FOCS'92),*Pittsburgh, PA, Oct. 1992, pp. 703-713. Rewritten as John H. Reif and Steve R. Tate, "N-body simulation I: Fast algorithms for potential field evaluation and Trummer's problem". Tech. Report. #N-96-002, Univ. of North Texas, Dept. of Computer Science (1996). [PostScript] [PDF] - William L. Hightower, Jan Prins,
and John H. Reif, Implementations of Randomized Sorting on Large Parallel
Machines.
*4th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'92)*, San Diego, CA, pp. 158-167, July 1992. [PDF] - Yijie Han, Victor Y. Pan, and John
H. Reif, Efficient Parallel Algorithms for Computing All Pair Shortest
Paths in Directed Graphs. University of Kentucky Technical Report
204-92.
*4th Annual ACM Symposium on Parallel Algorithms and Architectures*, San Diego, CA, July 1992, pp. 353-362. Published in Algorithmica, Vol 17, pp. 399-415, 1997. [PDF] - John H. Reif and Hongyan Wang,
Social Potential Fields: A Distributed Behavioral Control for Autonomous
Robots,
*Workshop on Algorithmic Foundations of Robotics (WAFR'94)*, San Francisco, California, February, 1994; The Algorithmic Foundations of Robotics, A.K.Peters, Boston, MA. 1995, pp. 431-459. Published in Robotics and Autonomous Systems, Vol. 27, no.3, pp.171-194, (May 1999). [PostScript] [PDF] - John H. Reif and Steve R. Tate,
Dynamic Algebraic Algorithms,
*Proceedings of the**5th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'94),*TX, Jan. 1994. pp.290-301. Published as On Dynamic Algorithms for Algebraic Problems, Journal of Algorithms, Volume 22, Number 2, pp. 347-371, February 1997. [PostScript] [PDF] - John H. Reif and Steve R. Tate,
Dynamic Parallel Tree Contraction,
*5th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'94)*, Cape May, NJ, June 1994. pp.114-121. Revised version submitted for journal publication. [PDF] - Deganit Armon and John H. Reif, A
Dynamic Separator Algorithm with Applications to Computational Geometry
and Nested Dissection,
*3rd Annual Workshop on Algorithms and Data Structures (WADS '93)*, Montreal, Quebec, Canada, August, 1993, pp. 107-118. [PDF] - Selman Azhar, Greg J. Badros,
Arman Glodjo, Ming Kao, and John H. Reif, Data Compression Techniques for
Stock Market Prediction,
*Proceedings: IEEE Data Compression Conference (DCC'94)*, Snowbird, UT, IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), March 1994, pp. 72-82. [PDF] - Joseph Cheriyan and John H. Reif,
Parallel and Output Sensitive Algorithms for Combinatorial and Linear
Algebra Problems, 1992.
*4th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'93*), Velon, Germany, July 1993, p.50-56. Published as John H. Reif, Parallel Output Sensitive Algorithms for Combinatorial and Linear Algebra Problems,*Journal of Computer and System Sciences*, Vol. 62, May 2001, pp. 398-412. [PostScript] [PDF] - Sotiris E. Nikoletseas, John H.
Reif, Paul G. Spirakis, Moti Yung, Stochastic Graphs Have Short Memory:
Fully Dynamic Connectivity in Poly-Log Expected Time.
*Proceedings of the 22nd Annual Colloquium on Automata, Languages and Programming (ICALP'95)*, Szeged, Hungary, July 1995, pp. 159-170. [PDF] - Steve R. Tate and John H. Reif,
The Complexity of N-body Simulation,
*Proceedings of the 20th Annual Colloquium on Automata, Languages and Programming (ICALP'93)*, Lund, Sweden, July, 1993, pp. 162-176. [PostScript] [PDF] - Tassos Markas and John H. Reif,
Multispectral Image Compression Algorithms,
*Proceedings: IEEE Data Compression Conference**(DCC'93)*, Snowbird, UT, IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), pp. 391-400, March 1993. [PDF] - Peter H. Mills, Jan Prins, and
John H. Reif, Rate Control as a Language Construct for Parallel and
Distributed Programming, Proc. IEEE Workshop on Parallel and Distributed
Real-Time Systems (IPPS'93), pp. 164-170, 1993. [PostScript] [PDF]
- Richard Barakat and John H. Reif,
Diffraction Realization of an Optical Expander, (1993). [PDF]
- Lars S. Nyland, Jan F. Prins, and
John H. Reif, A Data Parallel Implementation of the Adaptive Fast
Multipole Algorithm.
*Dartmouth Institute for Advanced Graduate Studies (DAGS '93),*Hanover, NH, June, 1993, pp. 111-123. [PostScript] [PDF] - Sefeng Chen and John H.
Reif, Using difficulty of prediction to decrease computation: fast
sort, priority queue and convex hull on entropy bounded inputs,
*34th Annual IEEE Conference on Foundations of Computer Science (FOCS '93) Proceedings*, November 1993, Palo Alto, CA, pp. 104-112. [PDF] - Andrew Neff and John H. Reif,
An
*O*(*n^{*1+epsilon} log*b*) Algorithm for the Complex Roots Problem.*35th Annual IEEE Conference on Foundations of Computer Science (FOCS '94) Proceedings*, Santa Fe, NM, November 1994. pp. 540-547. Improved Paper Published as An Efficient Algorithm for the Complex Roots Problem, Journal of Complexity, 12(2) pp. 81-115, (June 1996). [PostScript] [PDF] - Andrew Goldberg, Jan Prins,
Rickard Faith, Zhiyong Li, Peter H. Mills, Lars S. Nyland, Daniel Palmer,
John H. Reif, James Riely, and Stephen Westfold, The Proteus System for
the Development of Parallel Applications. Prototyping and Software
Development (Malcolm C. Harrison, ed.), Chapter 6, pp. 151-190, Digital
Book, 1996. [PostScript] [PDF]
- Peter H. Mills, Lars S. Nyland,
J.F. Prins, and John H. Reif, Software Issues in High-Performance
Computing and a Framework for the Development of HPC Applications.
In
*Developing a Computer Science Agenda for High Performance Computing*(U. Vishkin, ed.) pp. 110-117, ACM, 1994. [PostScript] [PDF] - Andrew Goldberg, Peter H. Mills,
Lars S. Nyland, Jan F. Prins, John H. Reif, and J. Riely, Specification
and Development of Parallel Algorithms with the Proteus
System, Specification of Parallel Algorithms,
*DIMACS Series in Discrete Mathematics and Theoretical Computer Science*, AMS Press, Vol. 18, 1994, pp. 383-399. [PostScript] [PDF] - Victor Y. Pan and John H. Reif,
Generalized Compact Multi-grid,
*Computers Math Applications, Volume*25, Number 9, pp. 3-5, May 1993. [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]

- Sefeng Chen and John H. Reif, Fast
Pattern Matching for Entropy Bounded Text.
*Proceedings: IEEE Data Compression Conference (DCC'95)*Snowbird, UT, IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), March 1995, pp. 282-301. [PDF] - John H. Reif, Efficient Parallel
Solution of Sparse Eigenvalue and Eigenvector Problems,
*Proceedings of the 36th Annual IEEE Symposium on Foundations of Computer Science (FOCS'95)*Milwaukee, WI, October 23-25, 1995, pp. 123-132. Published as Efficient Parallel Computation of the Characteristic Polynomial of a Sparse, Separable Matrix, Algorithmica, 29: 487-510 (2001). [PDF] - Akitoshi Yoshida, Jannick P. Rolland and John H. Reif,
Design and Applications of a High Resolution Insert Head-Mounted
Display.
*IEEE Virtual Reality Annual International Symposium (VRAIS'95)*, Research Triangle Park, NC, March 11-15, 1995, pp. 84-93. [PostScript] [PDF] Also, Jannick P. Rolland and Akitoshi Yoshida, and John H. Reif, Optical design and analysis of a head-mounted display with a high-resolution insert, (Novel Optical Systems Design and Optimization, Jose M. Sasian; Ed.,), Proc. SPIE Vol. 2537, pp. 71-82, Aug. 1995. Published as Jannick P. Rolland, Akitoshi Yoshida, Larry D. Davis, and John H. Reif, High resolution inset head-mounted display, Applied Optics: Optical Technology and Biomedical Optics, 37(19), 4183-4193 (1998). [PDF] - Sandeep K. S. Gupta, Zhiyong Li,
and John H. Reif, Generating Efficient Programs for Two-Level Memories
from Tensor-Products.
*Proceedings of the 7th IASTED/ISMM International Conference on Parallel and Distributed Computing and Systems*Washington DC, October 1995, pp. 510-513. [PostScript] [PDF] - John H. Reif, Parallel
Biomolecular Computation: Models and Simulations.
*Proceedings: 7th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'95)*Santa Barbara, CA, July 1995, pp. 213-223. Published in Algorithmica, special issue on Computational Biology, Vol. 25, No. 2, 142-176, 1999. [PDF] [PostScript] and [PostScriptFigures] - John H. Reif, Work Efficient
Parallel Solution of Toeplitz Systems and Polynomial GCD.
*Proc. of the 27th ACM Symposium on Theory of Computing (STOC 95)*, Las Vegas, NV, May 29-June 1, 1995, pp. 751-761. Revised as Efficient Parallel Factorization and Solution of Structured and Unstructured Linear Systems,*Journal of Computer and System Sciences*,*Vol. 71, Issue 1 (July 2005), pp. 86 - 143*. [PDF] [PDF] - Sandeep K. S. Gupta, Zhiyong Li,
and John H. Reif, Synthesizing Efficient Out-of-Core Programs for Block
Recursive Algorithms using Block-Cyclic Data Distributions. P
*roceedings of the 1996 International Conference on Parallel Processing*, Bloomingdale, IL, Vol. II, pp. 142-149, (August 1996). Published in*IEEE Transactions on Parallel and Distributed Systems*, Vol. 10, No. 3, March 1999, pp. 297-315. [PDF] or [PDF] - Lars S. Nyland, Jan Prins, Andrew
Goldberg, Peter H. Mills, John H. Reif, and Robert Wagner. A Refinement Methodology
for Developing Data-Parallel Applications, Second International
Euro-Par Conference (Euro-Par'96 Parallel Processing), Lyon, France,
Springer Lecture Notes in Computer Science, pp.145-150, 1996. [PDF]
- Sefeng Chen and John H. Reif,
Compression of Trees and Digraphs, Abstract,
*Proceedings: IEEE Data Compression Conference (DCC'96),*Snowbird, UT, James A. Storer, Martin Cohn (Eds.), IEEE Computer Society Press, March 1996. [PDF] - John H. Reif and Hongyan
Wang, Nonuniform Discretization for Kinodynamic motion planning
and its applications,
*Workshop on Foundations of Robotics,*Toulouse, France, July 1996, pp. 97-112. Published in SIAM Journal of Computing (SICOMP), Volume 30, No. 1, pp. 161-190, (2000). [PostScript] [PDF] - Zhiyong Li, Peter H. Mills, and
John H. Reif, Models and Resource Metrics for Parallel and Distributed
Computation,
*Proc. 28th Annual Hawaii International Conference on System Sciences*(HICSS-28 Parallel Algorithms Software Technology Track), Wailea, Maui, Hawaii, pp. 133-143, January 3-6, 1995. Published in*Parallel Algorithms and Applications*, Vol. 8, pp. 35-59, 1996. [PostScript] [PDF] - Erol Gelenbe, Nestor Schmajuk,
John Staddon, and John H. Reif, Autonomous Search and the Search for
Robots and Mines: A Survey, Robotics and Autonomous Systems, Vol. 22, pp.
23-33. (November 1997). [PostScript] [PDF]
- John H. Reif, Approximate Complex
Polynomial Evaluation in Near Constant Work Per Point. Proc. 29th ACM
Symposium on Theory of Computing (STOC97), El Paso, Texas, pp. 30-39 (May
4-6, 1997). Published in
*SIAM Journal of Computing (SICOMP),*Vol. 28, Number 6, pp. 2059-2089, 1999. [PostScript] [PDF] - John H. Reif, Efficient
Approximate Solution of Sparse Linear Systems, Published in
*Computers and Mathematics with Applications*, Vol. 36, No. 9, Nov. 1998, pp. 37-58. [PostScript] [PDF] (Also, see errata, Computers and Mathematics with Applications, Vol. 38, No. 9, 1999, pp. 141-141. [PDF]) - John H. Reif and Steve R. Tate,
Fast spatial decomposition and closest pair computation for limited
precision input, Journal of Algorithmica, Volume 28, Number 3, pp. 271-287
(2000). [PDF] or [PostScript] [PDF]
- Sefeng Chen and John H. Reif, Fast
and Compact Fast and Compact Volume Rendering in the Compressed
Transform,
*Proceedings: IEEE Data Compression Conference (DCC'97)*Snowbird, UT, James A. Storer, Martin Cohn (Eds.), IEEE Computer Society Press, March 1997, pp. 271-280. [PDF] - John H. Reif and Doreen Yen,
Derivation of Parallel Graph Connectivity Algorithms via Stream
Contraction, Duke University Technical Report, 1989. [PDF]
- John H. Reif, Local Parallel
Biomolecular Computation, Proc. DNA-Based Computers, III: University of
Pennsylvania, June 23-26, 1997. DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, H. Rubin and D. H. Wood, editors. American
Mathematical Society, Providence, RI, vol. 48, 1999, pp. 217-254. [PDF] Revised as invited paper of
special issue "Biomolecular
Computing - From Theory to Practical Applications"
*International Journal of Unconventional Computing*, Vol. 8, pp. 459-507 (2014). [PDF] or [PDF] - John H. Reif, On the Impossibility
of Interaction-Free Quantum Sensing for Small I/O Bandwidth,
*Information and Computation,*Jan 2000, pp. 1-20. [PDF] - John H. Reif, (Yin, Guo et
al. 2004)s: Robust, Adaptive and Dynamic Motion, 19th NSF Design and
Manufacturing Grantees Conference, Monterrey, Mexico, Jan 1998. [PostScript] [PDF]
- John H. Reif and Sandeep Sen,
Parallel Computational Geometry: An approach using randomization.
Published as Chapter 8 in
*Handbook of Computational Geometry,*Edited by Jorge Urrutia and Jörg-Rudiger Sack, Elsevier Science Publishing, Amsterdam, the Netherlands, pp. 765-828. 1999. [PDF] or [PDF] - John H. Reif, Paradigms for
Biomolecular Computation,
*First International Conference on Unconventional Models of Computation*, Auckland, New Zealand, January 5-9, 1998. Published*in Unconventional Models of Computation*, (edited by C.S. Calude, J. Casti, and M.J. Dinneen), DMTCS Series, Springer-Verlag, Singapore, January 1998, pp. 72-93. [PostScript] [PDF] - John H. Reif and James A. Storer,
Optimal Lossless Compression of a Class of Dynamic Sources, Data
Compression Conference (DCC'98), Snowbird, UT, James A. Storer, Martin
Cohn (Eds.), IEEE Computer Society Press, pp. 501-510, March, 1998. Published
as Optimal Encoding of Non-stationary Sources, Special Issue of
Information Sciences, Volume 135, pp. 87-105 (2001). [PDF]
- John H. Reif and Hongyan Wang, The
Complexity of the Two Dimensional Curvature-Constrained Shortest-Path
Problem,
*Third International Workshop on Algorithmic Foundations of Robotics**(WAFR98),*Pub. by A. K. Peters Ltd, Houston, Texas, pp. 49-57, June, 1998. [PostScript] [PDF] - John H. Reif and Zheng Sun, The
Computational Power of Frictional Mechanical Systems,
*Third International Workshop on Algorithmic Foundations of Robotics*,*(WAFR98),*Pub. by A. K. Peters Ltd, Houston, Texas, pp. 223-236, Mar. 5-7 1998. Published as On Frictional Mechanical Systems and Their Computational Power, SIAM Journal of Computing (SICOMP), Vol. 32, No. 6, pp. 1449-1474, (2003). [PDF] or [PDF]. Talk: [HTML] - A. Gehani and John H. Reif, Micro
Flow Bio-Molecular Computation, 4th DIMACS Workshop on DNA Based
Computers, University of Pennsylvania, June 15-19, 1998.
*DNA Based Computers, IV, DIMACS Series in Discrete Mathematics and Theoretical Computer Science,*(ed. H. Rubin), American Mathematical Society, 1999. Also in a special issue of Biosystems, Journal of Biological and Informational Processing Sciences, Vol. 52, Nos. 1-3, (Edited By L. Kari, H. Rubin, and D. H. Wood), pp. 197-216, (October 1999). [PostScript] [PDF] or [PDF] Talk: [PDF] - John H. Reif, Alternative
Computational Models: A Comparison of Biomolecular and Quantum
Computation, Invited paper, 18th
*International Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS1998),*Chennai, India (December, 17-19, 1998). [PDF] - John H. Reif and Zheng Sun,
Nano-Robotics Motion Planning and Its Applications in Nanotechnology and
Biomolecular Computing,
*NSF Design and Manufacturing Grantees Conference,*Jan 5-8, 1999. [HTML] - Thomas H. LaBean, Hao Yan, Jens
Kopatsch, Furong Liu, Erik Winfree, John H. Reif and Nadrian C. Seeman,
The construction, analysis, ligation and self-assembly of DNA triple
crossover complexes,
*Journal of American Chemistry Society(JACS)*122, pp. 1848-1860 (2000). [PDF] - John H. Reif and Sukhendu
Chakraborty, Efficient and Exact Quantum Compression, Journal of
Information and Computation, Vol. 205, pp. 967-981 (2007). [PDF] [PDF]
- John H. Reif, Quantum Computing.
In book “Bio-inspired and Nanoscale Integrated Computing”, Chapter 3, pp.
67-110 (edited by Mary Mehrnoosh Eshaghian-Wilner), Publisher:
Wiley, Hoboken, NJ, USA, (February 2009). [PDF]
- John Fischer and John H. Reif,
Nonparametric Multiscale Multimodal Model for Detection/Recognition,
Multi-Modality Image Fusion Conference, Rochester, NY, Oct 6-7, 1999. [PDF]
- A. Gehani, Thomas H. LaBean, and
John H. Reif, DNA-based Cryptography, Proc. DNA Based Computers V:
Cambridge, MA, June 14-16, 1999. Published in DIMACS Series in Discrete
Mathematics and Theoretical Computer Science, Volume 54, edited by Erik
Winfree and D.K. Gifford, American Mathematical Society, Providence, RI,
pp. 233-249, (2000). [PDF] Talk: [PDF]. Published as an invited chapter
in "Aspects of Molecular Computing - Essays dedicated to Tom
Head on the occasion of his 70th Birthday", Springer Verlag
series in Natural Computing (edited by N. Jonoska, G. Paun and
G. Rozenberg) LNCS 2950 Festschrift, Springer, pp. 167-188, (2004). [PDF]
- Thomas H. LaBean, Erik Winfree,
and John H. Reif, Experimental Progress in Computation by Self-Assembly of
DNA Tilings, Proceeding of DNA Based Computers V: Cambridge, MA, June
14-16, 1999. Published in DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, Volume 54, edited by Erik Winfree and D.K.
Gifford, American Mathematical Society, Providence, RI, pp. 123-140,
(2000). [PostScript] [PDF] Talk: [HTML Lecture]
- John H. Reif and Zheng Sun. An
efficient approximation algorithm for weighted region shortest path
problem. In
*Proceedings of the 4th Workshop on Algorithmic Foundations of Robotics (WAFR2000),*A. K. Peters Ltd Publishers, Hanover, New Hampshire, pp. 191-203, Mar. 16-18 2000. [PDF] [PostScript]. Published as Zheng Sun and John H. Reif, On Finding Approximate Optimal Paths in Weighted Regions, Journal of Algorithms, Volume 58, Number 1, pp. 1-32, January 2006. [PDF] - John H. Reif and Zheng Sun.
Movement planning in the presence of flows. In
*Proceedings of the 7th International Workshop on Algorithms and Data Structures*(WADS2001), volume 2125 of*Lecture Notes in Computer Science*, pp. 450-461, Brown University, Providence, RI, August 8-10, (2001). Published in Algorithmica, Volume 39, Number 2, pp. 127-153, February 2004. [PDF] or [PDF]. Talk: [PDF] - John H. Reif and Thomas H. LaBean,
Computationally Inspired Biotechnologies: Improved DNA Synthesis and
Associative Search Using Error-Correcting Codes and Vector-Quantization,
Sixth International Meeting on DNA Based Computers (DNA6)
*, Leiden, The Netherlands (June 2000).*DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Edited by A. Condon and G. Rozenberg. Lecture Notes in Computer Science, Springer-Verlag, Berlin Heidelberg, vol. 2054, pp. 145-172 (2001) [PostScript] [PDF] Talk: [PDF] - John H. Reif, Thomas H. LaBean,
and Nadrian C. Seeman, Challenges and Applications for Self-Assembled DNA
Nanostructures, Proc. Sixth International Workshop on DNA-Based Computers,
Leiden, The Netherlands, June 13-17, 2000. Published in DIMACS Series in
Discrete Mathematics and Theoretical Computer Science, Edited by A. Condon
and G. Rozenberg. Lecture Notes in Computer Science, Springer-Verlag,
Berlin Heidelberg, vol. 2054, 2001, pp. 173-198. [PostScript] [PDF] Talk: [PDF] [PPT]
- Chengde Mao, Thomas H. LaBean,
John H. Reif, Nadrian C. Seeman, Logical Computation Using
Algorithmic Self-Assembly of DNA Triple-Crossover Molecules, Nature, vol.
407, pp. 493-495 (Sept. 28 2000); C. Erratum: Nature 408, 750-750 (2000).
[PDF] or [PDF]
- John H. Reif and Thomas H. LaBean,
and Nadrian C. Seeman. Programmable Assembly at the Molecular Scale:
Self-Assembly of DNA Lattices, Invited paper, 2001 IEEE International
Conference on Robotics and Automation (ICRA2001)
*,*Seoul, Korea, ed. Lee Beom, pp. 966-971 (May, 2001). [PDF] - Zheng Sun and John H. Reif.
BUSHWHACK: An approximation algorithm for minimal paths through
pseudo-Euclidean spaces. In
*Proceedings of the 12th Annual International Symposium on Algorithms and Computation*(ISAAC01), Christchurch, New Zealand, Dec 19-21, 2001, Volume 2223 of*Lecture Notes in Computer Science*, pp. 160-171, Dec, 2001. Published in IEEE Transactions on Systems, Man, and Cybernetics (SMC), Part B: Cybernetics, Vol. 37, No. 4, pp. 925-936 (2007). [PDF] [PDF] - John H. Reif, Thomas H. LaBean, M.
Pirrung, V. Rana, B. Guo, K. Kingsford, and G. Wickham, 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. Lecture Notes in Computer Science, Springer-Verlag, New York, Volume 2340, pp. 231-247, (2002). [PostScript] [PDF] Talk: [PDF] [PPT]. Also published as John H. Reif, Michael Hauser, Michael Pirrung, and Thomas LaBean, Application of Biomolecular Computing to Medical Science: A Biomedical Database System for Storage and Retrieval of Genetic Information and Material, Chapter 3 of Complex Systems Science in Biomedicine (Edited by Thomas S. Deisboeck and J. Yasha Kresh), International Topics in Biomedical Engineering Series, Springer Publishers, New York, Chapter 3, pp. 701-735, (2005). ISBN: 0-387-30241-7. [PDF] or [PDF]. Talk: [PDF][PPT] - John H. Reif, DNA Lattices: A
Method for Molecular Scale Patterning and Computation, special issue on
Bio-Computation, Computer and Scientific Engineering Magazine, IEEE Computer
Society, Vol. 4, No. 1, February 2002, pp. 32-41. [PostScript][PDF]
- John H. Reif, The Emerging Discipline
of Biomolecular Computation in the US, invited paper to the special
issue on Biomolecular Computing, New Generation Computing, edited by
Masami Hagiya, Masayuki Yamamura, and Tom Head, Vol. 20, No. 3, pp.
217-236, (2002). [PostScript][PDF] or [PDF]
- John H. Reif, Molecular Assembly
and Computation: From Theory to Experimental Demonstrations, plenary
paper, Twenty Ninth International Colloquium on Automata, Languages, and
Programming(ICALP), Málaga, Spain (July 8, 2002). Lecture Notes in
Computer Science, New York, Volume 2380, pp. 1-21, (2002). [PostScript][PDF] Talk: [PDF] [PPT]
- John H. Reif, The Design of
Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA. DNA Based
Computers (DNA8), Sapporo, Japan, June 10-13, 2002, (Edited by Masami
Hagiya and Azuma Ohuchi), Lecture Notes in Computer Science, No. 2568,
Springer-Verlag, New York, (2003), pp. 22-37. Published in Natural
Computing, DNA8 special issue, Vol. 2, p 439-461, (2003). [PDF] or [PostScript][PDF] Talk: [
__PDF__] - Dage Liu, John H. Reif, Thomas H.
LaBean, DNA Nanotubes, Construction and Characterization of Filaments
Composed of TX-tile Lattice. DNA Based Computers (DN
**A**8), Sapporo, Japan, June 10-13, 2002, (Edited by Masami Hagiya and Azuma Ohuchi), Lecture Notes in Computer Science, No. 2568, Springer-Verlag, New York, (2003), pp. 10-21. Published as DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires, Proceedings of the National Academy of Science(PNAS), Vol. 101, No. 3, pp. 717-722, (January 20, 2004). PubMed PMID: 14709674. [PDF] - John H. Reif, DNA Computation -
Perspectives: Successes and Challenges, Science, 296: 478-479, April 19,
2002. PubMed PMID: 11964464. [PostScript][PDF]
- Zheng Sun and John H. Reif, On
Finding Energy-minimizing Paths on Terrains for a Mobile Robot, 2003 IEEE
International Conference on Robotics and Automation(ICRA2003), Taipei,
Taiwan, pp. 3782-3788, May 12-17, 2003. Published in IEEE
Transaction on Robotics, Volume: 21, Issue: 1, February 2005, pp. 102-114.
[PDF]
- D. Hsu, T. Jiang, John H. Reif,
and Zheng Sun, The Bridge Test for Sampling Narrow Passages with
Probabilistic Roadmap Planners, 2003 IEEE International Conference on
Robotics and Automation(ICRA2003), Taipei, Taiwan, Vol.3, pp. 4420 – 4426,
Sept. 14-19, 2003. Published as Zheng Sun, D. Hsu, T. Jiang, H.
Kurniawati, and J.H.Reif, Narrow Passage Sampling for Probabilistic
Roadmap Planning, IEEE Transactions on Robotics, Volume 21, No. 6, Dec.
2005. pp. 1105–1115. [PDF]
- John H. Reif and Zheng Sun, On
Boundaries of Highly Visible Spaces and Applications, 14th Symposium
on Fundamentals of Computation Theory, Malmö Högskola, Sweden, August
12-15, 2003, Springer-Verlag Lecture Notes in Computer Science, 2003.
Invited paper published in Theoretical Computer Science, Volume 354, Issue
3, (4 April 2006), pp. 379-390. [PDF] [PDF]
- Hao Yan, Thomas H. LaBean, Liping
Feng, and John H. Reif, Directed Nucleation Assembly of Barcode Patterned
DNA Lattices, Proceedings of the National Academy of
Science(PNAS), Volume 100, No. 14, pp. 8103-8108, July 8, (2003). PubMed
PMID: 12821776. [PostScript] [PDF]
- Hao Yan, Liping Feng, Thomas H.
LaBean, and John H. Reif, DNA Nanotubes,
*Parallel Molecular Computation of Pair-Wise XOR Using DNA String Tile,*Ninth International Meeting on DNA Based Computers (DNA9), Madison, Wisconsin, June 2-4, 2003, (Edited by Junghuei Chen and John H. Reif), Abstract in Lecture Notes in Computer Science, Springer-Verlag, New York, (2003). Published as Parallel Molecular Computations of Pairwise Exclusive-Or (XOR) Using DNA "String Tile" Self-Assembly in Journal of American Chemistry Society (JACS), Vol. 125, No. 47, pp. 14246-14247, 2003. PubMed PMID: 14624551. [PDF] or [PDF]; Supporting Information: [PDF] - Hao Yan, Sung Ha Park, Liping
Feng, John H. Reif, and Thomas H. LaBean,
*4x4 DNA Tile and Lattices: Characterization, Self-Assembly and Metallization of a Novel DNA Nanostructure Motif*, Ninth International Meeting on DNA Based Computers (DNA9), Madison, Wisconsin, June 2-4, 2003, (Edited by Junghuei Chen and John H. Reif), Lecture Notes in Computer Science, Springer-Verlag, New York, (2003). Published as Hao Yan, Sung Ha Park, Gleb Finkelstein, John H. Reif, and Thomas H. LaBean, DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires, Science, Vol. 301, pp. 1882-1884, Sep 26 2003. PubMed PMID: 14512621. [PDF] Supporting Materials: [PDF] Supplemental Information: [PDF] - Liping Feng, Sung Ha Park, John H.
Reif, and Hao Yan, A Two-State DNA Lattice Switched by DNA Nanoactuator,
Angewandte Chemie [International Edition], Vol. 42, pp. 4342-4346,
Sept. 2003. PubMed PMID: 14502706. [PDF] Supplemental Information: [PDF]
- Zheng Sun and John
H. Reif, Adaptive and Compact Discretization for Weighted Region Optimal
Path Finding. 14th Symposium on Fundamentals of Computation Theory, Malmö
Högskola, Sweden, August 12-15, 2003, Springer-Verlag Lecture Notes in
Computer Science, Vol. 2751, pp. 258-270, 2003. [PostScript] [
*PDF*]. - Tinging Jiang and John
H. Reif, Efficient Methods for Stochastic Simulations of
Biomolecular Motions, submitted for publication, July, 2003. [PDF]
- H. Li, S.H. Park, John H. Reif,
Thomas H. LaBean, Hao Yan, DNA-Templated Self-Assembly of Protein and
Nanoparticle Linear Arrays, Journal of American Chemistry Society (JACS),
Vol. 126, No. 2, pp. 418-419, 2004. PubMed PMID: 14719910. [PDF]. Supporting Information: [PDF]
- Hao Yan, Peng Yin, Sung Ha Park,
Hanying Li, Liping Feng, Xiaoju Guan, Dage Liu, John H. Reif, & Thomas
H. LaBean (2004) Self-Assembled DNA Structures for Nanoconstruction.
International Symposium on DNA-Based Molecular Electronics, Jena, Germany,
May, 2004. Fritzsche, W. eds. AIP Conference Proceedings, 725, American
Institute of Physics. pp. 43-52. [PDF]
- John H. Reif, Sudheer Sahu, Peng
Yin, Compact Error-Resilient Computational DNA Tiling Assemblies, Tenth
International Meeting on DNA Based Computers (DNA10), Milano, Italy,
June 7-10, 2004. Lecture Notes in Computer Science (Edited by C Ferretti,
G. Mauri and C. Zandron), Vol. 3384, Springer-Verlag, New York,
(2005), pp. 293-307. Published as an invited chapter in text "Nanotechnology:
Science and Computation”, Springer Verlag series in Natural
Computing (edited by J. Chen; N. Jonoska and G. Rozenberg),
Springer-Verlag Berlin, Germany, pp. 79-104, 2006. [PDF] Talk: [PDF] [PPT]
- Peng Yin, Andrew J. Turberfield,
Sudheer Sahu, John H. Reif, Designs for Autonomous Unidirectional Walking
DNA Devices, Tenth International Meeting on DNA Based Computers
(DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in Computer Science
(Edited by C Ferretti, G. Mauri and C. Zandron), Vol. 3384, Springer-Verlag,
New York, (2005), pp. 410-425. [PDF] Talk: [PDF] [PPT]
- Peng Yin, Hao Yan, Xiaoju G.
Daniel, Andrew J. Turberfield, John H. Reif, A Unidirectional DNA Walker
Moving Autonomously Along a Linear Track, Angewandte Chemie [International
Edition], Volume 43, Number 37, Sept. 20, 2004, pp. 4906-4911. PubMed
PMID: 15372637. [PDF] or [PDF] Supplemental Information: [PDF] Abstract: [PDF] Talk: [PDF] [PPT]
- Peng Yin, Andrew J. Turberfield,
John H. Reif, Design of an Autonomous DNA Nanomechanical Device Capable of
Universal Computation and Universal Translational Motion, Tenth
International Meeting on DNA Based Computers (DNA10), Milano, Italy,
June 7-10, 2004. Lecture Notes in Computer Science (Edited by C Ferretti,
G. Mauri and C. Zandron), Vol. 3384, Springer-Verlag, New York,
(2005), pp. 426-444. [PDF] Talk: [PDF] [PPT]
- Peng Yin, Bo Guo, Christina
Belmore, Will Palmeri, Erik Winfree, Thomas H. LaBean, John H. Reif,
TileSoft: Sequence Optimization Software For Designing DNA Secondary
Structures, Duke University Computer Science Department Technical
Report TR-CS-2004-09. [PDF] Talk: [PDF] [PPT]
- John H. Reif, DNA-Based
Nano-Engineering: DNA and its Enzymes as the Engines of Creation at the
Molecular Scale, Invited Talk, Abstract, Preliminary Proceedings, Tenth
International Meeting on DNA Based Computers (DNA10), Milano, Italy, (June
7-10, 2004). Abstract: [PDF] Talk: [PDF] [PPT]
- John H. Reif, Thomas LaBean,
Sudheer Sahu, Hao Yan, Peng Yin, Design, Simulation, and Experimental
Demonstration of Self-Assembled DNA Nanostructures and DNA Motors,
Unconventional Programming Paradigms: International Workshop UPP 2004, Le
Mont Saint Michel, France, September 15-17, 2004. Published by
Springer-Verlag Berlin Heidelberg, edited by Jean-Pierre Banâtre, Pascal
Fradet, Jean-Louis Giavitto, Olivier Michel, Lecture Notes for Computer
Science (LNCS) 3566, pp. 173-187, (2005). [PDF] Talk: [PDF] [PPT]
- Sung Ha Park, Hao Yan, John H.
Reif, Thomas H LaBean, and Gleb Finkelstein, Electronic nanostructures
templated on self-assembled DNA scaffolds, Nanotechnology 15 pp. S525–S527
(2004). [PDF]
- Sung Ha Park, Peng Yin, Yan Liu,
John H. Reif, Thomas LaBean, and Hao Yan, Programmable DNA Self-assemblies
for Nanoscale Organization of Ligands and Proteins,
*Nano Letters*(Communication), Volume*5*, Number 4, pp. 729-733, (2005). PubMed PMID: 15826117. [PDF]; Supplemental Information: [PDF] - Sung Ha Park, Robert Barish, Hanying Li,
John H. Reif, Gleb Finkelstein, Hao Yan and Thomas LaBean, Three-Helix
Bundle DNA Tiles Self-Assemble into 2D Lattice or 1D Templates for Silver
Nanowires, Nano Letters (Communication), Volume 5, Number 4, pp. 693-696
(2005). PubMed PMID: 15826110. [PDF] Supplemental Information: [
*PDF*] - Sung Ha Park, Constantin Pistol,
Sang Jung Ahn, John H. Reif, Alvin R. Lebeck, Chris Dwyer, and Thomas H.
LaBean, Finite-Size, Fully Addressable DNA Tile Lattices Formed by
Hierarchical Assembly Procedures, Angewandte Chemie [International
Edition], Volume 45, Issue 5, pp. 735-739, January 23, 2006. DOI:
10.1002/anie.200503797. [PDF]
- John H. Reif, Sudheer Sahu, and
Peng Yin, Complexity of Graph Self-Assembly in Accretive Systems and
Self-Destructible Systems, Eleventh International Meeting on DNA
Based Computers (DNA11), London, Ontario, Canada (June, 2005).
Springer-Verlag Lecture Notes for Computer Science (LNCS), NYC, NY,
(edited by Alessandra Carbone and Niles Pierce), Vol.
3892, Springer-Verlag, New York, (2006), pp. 257-274 [PDF]. Talk: [PPT]. Published in Theoretical
Computer Science, Volume 412, pp 1592-1605, (2011). DOI information:
10.1016/j.tcs.2010.10.034 [PDF].
- Peng Yin, Andrew J. Turberfield,
John H. Reif, Design of Autonomous DNA Cellular Automata, Eleventh
International Meeting on DNA Based Computers (DNA11), London,
Ontario, Canada (June, 2005). Springer-Verlag Lecture Notes for Computer
Science (LNCS), NYC, NY, (edited by Alessandra Carbone and Niles
Pierce), Vol. 3892, Springer-Verlag, New York, (2006), pp.
399-416 [PDF].
- Sudheer Sahu, Peng Yin and John H.
Reif, A Self-Assembly Model of Time-Dependent Glue Strength, Eleventh
International Meeting on DNA Based Computers (DNA11), London,
Ontario, Canada (June, 2005). Springer-Verlag Lecture Notes for Computer
Science (LNCS), NYC, NY, (edited by Alessandra Carbone and Niles
Pierce), Vol. 3892, Springer-Verlag, New York, pp. 290-304
(2006). Invited Chapter in "Algorithmic Bioprocesses"
(edited by A.Condon, D.Harel, J.N.Kok, A.Salomaa, and E.Winfree),
Published by Springer-Verlag, ISBN: 978-3-540-88868-0, pp. 185-204
(2009). [PDF] [PDF] Talk: [PPT]
- Peng Yin, Sudheer Sahu, Rizal
Hariadi, Harry M. T. Choi, Sung Ha Park, Bethany Walters, Thomas H.
LaBean, John H. Reif, On Constructing Tile-less DNA Ribbons and Tubes,
Abstract, Preliminary Proceedings, 12th International Meeting on DNA Computing
(DNA12), Seoul, Korea (June 5-9, 2006). [PDF] Published as: Peng Yin,
Rizal F. Hariadi, Sudheer Sahu, Harry M.T.Choi, Sung Ha Park, Thomas H.
LaBean, John H. Reif, Programming DNA Tube Circumferences, Science, Vol.
321. no. 5890, pp. 824–826 (August 8, 2008). DOI:
10.1126/science.1157312. [PDF] Supplemental Information: [PDF]
- Sudheer Sahu and John H. Reif,
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. Published
in DNA Computing: DNA12, Springer-Verlag Lecture Notes for Computer
Science (LNCS), Volume 4287 (edited by Chengde Mao and Takashi Yokomori),
Springer, Berlin Heidelberg, pp. 223-238 (2006). DNA12 Version: [PDF]. Talk: [PPT]. Published in Algorithmica,
Volume 56, Issue 4, pp. 480-504, Springer New York (April 2010), Full
Paper: [PDF] [
__PDF__]. - Sudheer Sahu, Bei Wang, Peng Yin,
John H. Reif, A Framework for Modeling DNA based Molecular Systems,
12th International Meeting on DNA Computing (DNA 12), Seoul, Korea, June
5-9, 2006. Published in DNA Computing: DNA12, Springer-Verlag Lecture
Notes for Computer Science (LNCS), Volume 4287 (edited by Chengde Mao
and Takashi Yokomori), Springer, Berlin Heidelberg, pp. 250-265
(2006). DNA12 Version: [PDF]. Published as Sudheer Sahu,
Bei Wang, John H. Reif, A Framework for Modeling DNA based Molecular
Systems. Computational and Theoretical Nanoscience, Volume
5, Number 11, pp. 2124-2134(11) (November 2008). Full
Paper: [PDF] Presentation: [PPT]
- Urmi Majumder, Sudheer Sahu,
Thomas LaBean, and John H. Reif, Design and Simulation of Self-Repairing
DNA Lattices, 12th International Meeting on DNA Computing (DNA 12), Seoul,
Korea, June 5-9, 2006, DNA Computing: DNA12, Springer-Verlag Lecture Notes
for Computer Science (LNCS), Volume 4287 (edited by Chengde Mao and
Takashi Yokomori), Springer, Berlin Heidelberg, pp. 195–214,
(2006). DNA12 Version: [PDF] Poster: [PDF]. Revised paper: Urmi
Majumder, Sudheer Sahu, Thomas LaBean, and John H. Reif, Toward Compact
Inherently Self-Repairing DNA Lattices Using Reversibility, submitted
for journal
publication (2014). [PDF]
- John H. Reif and Sam Slee,
Asymptotically Optimal Kinodynamic Motion Planning for Self-Reconfigurable
Robots, Seventh International Workshop on the Algorithmic Foundations of
Robotics (WAFR2006), NYC, New York, July 16-18,
2006. Published in Algorithmic Foundation of Robotics VII, Springer
Tracts in Advanced Robotics (Edited by S. Akella, N.M. Amato, W.H. Huang,
B. Mishra), Volume 47, Springer-Verlag Berlin, pp. 457–472, (Aug
2008). [PDF] Published as Asymptotically
Optimal Kinodynamic Motion Planning for a Class of Lattice-Style Modular
Self-Reconﬁgurable Robots, International Journal of Computational
Geometry & Applications (IJCGA), Vol. 21, No. 2, pp.
131-155 (2011). DOI: 10.1142/S0218195911003585 [PDF]
- Thomas H. LaBean, Kurt V. Gothelf,
and John H. Reif, Self-assembling DNA Nanostructures for Patterned
Molecular Assembly, invited chapter 5 in Nanobiotechnology II: More
Concepts and Applications, (edited by Chad A. Mirkin and Christof M.
Niemeyer), John Wiley & Sons Publishers, pp. 79-97, (2007). [PDF] DOI: 10.1002/9783527610389.ch5
- John H. Reif and Thomas H. LaBean,
Autonomous Programmable Biomolecular Devices Using Self-Assembled DNA
Nanostructures, invited paper, Fourteenth Workshop on Logic,
Language, Information and Computation (WoLLIC'2007), Rio de Janeiro,
Brazil, July 2-5, 2007, Springer-Verlag Lecture Notes for Computer
Science (LNCS), Volume 4576 - 0297, pp. 297-306. Published in Communications
of the ACM (CACM), Special Section entitled “New Computing Paradigms
(edited by Toshinori Munakata), Volume 50, Issue 9, pp. 46-53 (Sept
2007). Short version [PDF] Extended version [PDF] Talk: [PPT] [PDF]
- Urmi Majumder and John H. Reif, A
Framework for Designing Novel Magnetic Tiles Capable of Complex
Self-Assemblies, Conference on Unconventional Computation, Vienna,
Austria, Aug 25-26, 2008. Published in Unconventional Computing, Lecture
Notes in Computer Science number 105633, Springer, Berlin Heidelberg.
Conference Version: [PDF]. Revised paper submitted
for journal
publication as Barcoded
Magnetic Tiles for Complex Programmable Assemblies (2010). Full Paper: [PDF]
- John H. Reif and Thomas H. LaBean,
DNA Nanotechnology and its Biological Applications. In book “Bio-inspired
and Nanoscale Integrated Computing”, Chapter 13, pp. 349-375 (edited by
Mary Mehrnoosh Eshaghian-Wilner), Publisher: Wiley, Hoboken,
NJ, USA, (February 2009). [PDF]
- Ashish Gehani and John H. Reif,
Parameterizing Super-resolution Forensic Analysis of Video, 3rd IFIP
International Conference on Digital Forensics, Orlando, FL, Jan 28-31,
2007. Published as Super-Resolution Video Analysis for Forensic
Investigations, Advances in Digital Forensics, Chapter 20, Volume 32007,
pp. 228-229. [PDF]
- John H. Reif and Sam Slee, Optimal
Kinodynamic Motion Planning for Self-Reconﬁgurable Robots Between
Arbitrary 2D Conﬁgurations, Robotics: Science and Systems Conference,
Georgia Institute of Technology, Atlanta, GA, June 27-30, 2007. [PDF]
- John H. Reif and Sudheer Sahu,
Autonomous Programmable DNA Nanorobotic Devices Using DNAzymes, 13th
International Meeting on DNA Computing (DNA 13), Memphis, Tennessee,
June 4-8, 2007. In DNA Computing: DNA13 (edited by Max Garzon and Hao
Yan), Springer-Verlag Lecture Notes for Computer Science (LNCS), Springer,
Berlin Heidelberg, Volume 4848, pp. 66-78 (2008). DNA13
Version: [PDF] Talk: [PDF]. Published in Special
Journal Issue on Self-Assembly, Theoretical Computer Science (TCS),
Vol 410, Issue 15, pp. 1428-1439 (April 2009). Full Paper: [PDF] [PDF].
- Urmi Majumder, Thomas H LaBean,
and John H. Reif, Activatable Tiles for Compact Error-Resilient
Directional Assembly. 13th International Meeting on DNA Computing (DNA
13), Memphis, Tennessee, June 4-8, 2007. Conference Version: Activatable
Tiles: Compact, Robust Programmable Assembly and Other Applications, in
DNA Computing: DNA13 (edited by Max Garzon and Hao Yan), Springer-Verlag
Lecture Notes for Computer Science (LNCS), Springer, Berlin Heidelberg,
Volume 4848, pp. 15-25, (2008). [PDF] Talk: [PPT]. Published as: Urmi Majumder,
Sudhanshu Garg, Thomas H LaBean, and John H. Reif, Activatable Tiles for
Compact Robust Programmable Molecular Assembly and Other Applications, Natural Computing, Volume 15, Issue 4, pp. 611–634
(December 2016). DOI
10.1007/s11047-015-9532-3 [PDF] [PDF]
- Urmi Majumder, John H. Reif, and
Sudheer Sahu, Stochastic Analysis of Reversible Self-Assembly. Journal of
Computational and Theoretical Nanoscience, Volume 5, Number 7, pp.
1289-1305, July 2008. Full Paper: [PDF] [PDF].
- John H. Reif, Mechanical
Computation: it’s Computational Complexity and Technologies, invited
chapter, Encyclopedia of Complexity and System Science (edited by Robert
A. Meyers), in section:
Unconventional Computing (section editor: Andrew Adamatzky), Springer-Verlag, New York (2009),
pp. 1821-1836, ISBN: 978-0-387-75888-6.
DOI: 10.1007/978-0-387-30440-3_325. [HTML] [PDF] [PDF]. A revised version also
appears as Mechanical Computing:
The Computational Complexity of Physical Devices, invited chapter, Encyclopedia of
Complexity and System Science (edited by Andrew
Spencer), Springer-Verlag, Heidelberg, Germany. Springer-Verlag,
Heidelberg, Germany. Published online (2013) and in print in pp. 5466-5482
(2014). [HTML] [PDF] [PDF] [PDF] A further revised version also
appears as Mechanical Computing:
The Computational Complexity of Physical Devices, invited chapter, pp. 1-21, Encyclopedia of
Complexity and System Science (edited
by R.A.), Springer-Verlag, Heidelberg, Germany. Springer-Verlag,
Heidelberg, Germany (April 2017) [PDF] [PDF]
DOI: 10.1007/978-3-642-27737-5_325-4. Also appearing as Chapter
2 in book Unconventional Computing, pp. 35-55, (2018).
DOI: 10.1007/978-1-4939-6883-1_325 [PDF] [PDF]
- John H. Reif and Urmi Majumder,
Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular
Computation, Fourteenth International Meeting on DNA Based
Computers (DNA14), Prague, Czech Republic (June, 2008). Lecture
Notes for Computer Science (LNCS), NYC, NY, (edited by Ashish Goel
and Friedrich C. Simmel), Springer-Verlag, New York, (2009).
Conference Version: [PDF] Talk: [PDF] [PPT]. Invited Paper, Special
issue in Natural Computing, Vol. 9, Number 1, pp. 183-206, (March 2010).
Springer Netherlands, ISSN: 1567-7818 (Online), DOI:
10.1007/s11047-009-9148-6. Full Paper: [PDF] [PDF]
- Sudheer Sahu, Thomas H. LaBean and
John H. Reif, A DNA Nanotransport Device Powered by Polymerase ϕ29,
Nano Letters, 2008, 8 (11), pp 3870–3878, (October, 2008) DOI:
10.1021/nl802294d. [PDF] [PDF] supplementary material: [PDF]
- Thomas H. LaBean, Geetha Shetty,
Peng Yin, Erik A. Schultes, Harish Chandran, John H. Reif, A
Dendritic Nanostructure for DNA Detection, abstract, Proceedings of
the Sixth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices (FNANO09), Snowbird, Utah, Sciencetechnica, pp. 82-83
(April 2009). [PDF] Thomas H. LaBean, Geetha Shetty,
Hao Yan, Erik A. Schultes, Harish Chandran, John H. Reif, Target DNA
Detection by Strand Displacement and Deoxyribozymogen
Amplification, abstract, Proceedings of the Sixth Conference on
Foundations of Nanoscience: Self-Assembled Architectures and Devices
(FNANO09), Snowbird, Utah, Sciencetechnica, pp. 60-61 (April 2009). [PDF] Bishop Morgan A.,
Clare D. Thiem, Thomas E. Renz, Erik A. Schultes, Harish Chandran, John H
Reif, Structural Optimization of Dendritic DNA Self-Assembly, abstract,
Proceedings of the Sixth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO09), Snowbird, Utah,
Sciencetechnica, pp. 147-148 (April 2009). [PDF]
*Final Publication:*Harish Chandran, Abhijit Rangnekar, Geetha Shetty, Erik A Schultes, John H Reif, Thomas H LaBean, An Autonomously Self‐Assembling Dendritic DNA Nanostructure for Target DNA Detection, Biotechnology Journal, Wiley-VCH Verlag, Vol. 8, Number 2, pp. 221-227, (Feb, 2013). PMID: 22965937. DOI: 10.1002/biot.201100499. [PDF] (also published online Oct, 2012) - Nikhil Gopalkrishnan, Harish
Chandran and John Reif, 2D and 3D DNA Lattices Via Staggered Assembly of
the Double-Decker Tile, abstract, Digital Proceedings of the Ninth
Conference on Foundations of Nanoscience: Self-Assembled Architectures and
Devices (FNANO12), Snowbird, Utah, pp. 108 (April 2012).
- Harish Chandran, Nikhil
Gopalkrishnan, and John Reif, The Tile Complexity of Linear Assemblies,
36th International Colloquium on Automata, Languages and Programming
(ICALP 2009), July 5 - 12, 2009, Rhodes, Greece, Proceedings Part I
(edited by Susanne Albers, Alberto Marchetti-Spaccamela, Yossi Matias,
Sotiris Nikoletseas, and Wolfgang Thomas), Lecture Notes in Computer
Science, Springer-Verlag, Berlin, pp. 235-253 (2009). Published in SIAM
Journal of Computation (SICOMP), Society for Industrial Mathematics, Vol.
41, No, 4, pp. 1051-1073, (2012). [PDF] [PDF] Talk: [PPT] [PDF]
- John H. Reif and Thomas H. LaBean,
Engineering Natural Computation by Autonomous DNA-Based Biomolecular
Devices, Invited Chapter, Handbook of Natural
Computing, Chapter
39, Volume III, edited by Grzegor Rozenberg, Thomas Bäck, Joost
Kok, Springer-Verlag, Heidelberg, Germany, pp.1314-1354 (July,
2012), ISBN-10: 3540929096,
ISBN-13: 978-3-540-9-2909-3. [PDF] [PDF]
- John H. Reif and Urmi
Majumder, 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). Lecture Notes for Computer Science (LNCS), Vol 5877, NYC, NY,
(edited by Russell Deaton and Jin-Woo Kim), Springer-Verlag, New
York, pp 107-105, (2010) [PDF] [PDF]. Published in Natural Computing,
Vol 10, No. 1. pp 447-466 (2011). Talk: [PDF] [PPT] [Keynote].
- John Reif, Harish Chandran, Nikhil
Gopalkrishnan, and Thomas LaBean, Self-assembled DNA Nanostructures and
DNA Devices. Invited Chapter 14, pages 299-328, Nanofabrication Handbook
(Edited by Stefano Cabrini and Satoshi Kawata), Taylor and Francis
Group, New York, NY, ISBN13:9781420090529, ISBN10: 1420090526
(2012). [PDF] [PDF]
- Harish Chandran, Nikhil
Gopalkrishnan and John Reif, Tile Complexity of
Approximate Squares and Lower Bounds for Arbitrary Shapes, Algorithmica, Volume 66,
Issue 1 (2013), Page 1-17 (2013) (also published online Feb 22, 2012). ISSN 0178-4617, DOI
10.1007/s00453-012-9620-z. [PDF] [PDF]
- Nikhil Gopalkrishnan, Harish
Chandran and John Reif, 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. Lecture Notes for
Computer Science (LNCS), Vol. 6516, NYC, NY, (edited by Yasubumi
Sakakibara and Mi Yongli), Springer-Verlag, LNCS 6518, New York,
(Feb 2011), pp 59-70. ISBN: 978-3-642-18304-1 [PDF] [PDF] Talk: [PDF] [PPT]
- Sam Slee and John H. Reif,
Robomotion: Sam Slee and John H. Reif, Robomotion: Scalable, Physically
Stable Locomotion for Self-Reconfigurable Robots, Workshop on the
Algorithmic Foundations of Robotics (WAFR 2010), Singapore, Springer (Dec.
13-15 2010). [PDF]
- Urmi Majumder, Abhijit
Rangnekar, Kurt V. Gothelf, John H Reif and Thomas H LaBean, Design and
Construction of Double-Decker Tile as a Route to Three-Dimensional
Periodic Assembly of DNA, Journal American Chemical Society
(JACS), Vol. 133, no. 11, pp. 3843—3845 (Feb. 2011) [PDF] Supplementary Info: [PDF]
- Harish Chandran,
Nikhil Gopalkrishnan, and John Reif, DNA NanoRobotics, Chapter,
Nanorobotics: Current Approaches and Techniques, (edited by Constantinos
Mavroidis and Antoine Ferreira), Springer-Verlag, New York, NY, pp.
355-382 (Jan. 31, 2013). ISBN 13
**:**9781461421184, ISBN 10**:**1461421187 [PDF] [PDF] - John H. Reif, Perspectives:
Biochemistry: Scaling Up DNA Computation, Science, Vol. 332,
pp. 1156-1157 (June 3, 2011). DOI: 10.1126/science.1208068 [PDF]
- Harish Chandran, Nikhil
Gopalkrishnan, Andrew Philips and John Reif, Localized Hybridization
Circuits, International Conference on DNA Computing and Molecular
Programming, (DNA17), California Institute of Technology, Pasadena,
California, Sept 19-23, 2011, pp. 64-83. Lecture Notes for Computer
Science (LNCS), NYC, NY, (edited by Luca Cardelli and William Shih),
Springer-Verlag, LNCS, Berlin, Heidelberg, (2011). ISBN:
978-3-642-23637-2 [PDF] Revised as Neil Dalchau, Harish
Chandran, Nikhil Gopalkrishnan, Andrew Philips and John Reif, Probabilistic
Analysis of Localized DNA Hybridization Circuits, ACS Synthetic
Biology, Vol.
*4*, Issue 8, pp 898–913, (July, 2015). DOI:10.1021/acssynbio.5b00044 [PDF] [PDF] Supporting Info: [PDF] - Harish Chandran, Nikhil
Gopalkrishnan, Sudhanshu Garg, and John Reif, Biomolecular Computing
Systems - From Logic Systems to Smart Sensors and Actuators, Invited
Chapter 11, Molecular and
Biomolecular Information Processing (Editor: Evgeny Katz), Published by Wiley-VCH, Verlag
GmbH & Comp. KGaA, Weinheim, Germany, pp.
199-224, July 2012. ISBN 978-3-527-33228-1 Online ISBN: 9783527645480
DOI: 10.1002/9783527645480 [PDF] [PDF]
- Harish
Chandran, Nikhil Gopalkrishnan, Bernard Yurke, John Reif, Meta-DNA: Synthetic
Biology via DNA Nanostructures and Hybridization Reactions, Journal of the Royal
Society Interface, (published online Jan., 2012),
pp. 1742-5662 doi: 10.1098/rsif.2011.0819 [PDF] [PDF] [Supplement]. An expanded version appears
as Meta-DNA: A
DNA-Based Approach to Synthetic Biology, Chapter 7 in Book: A Systems Theoretic
Approach to Systems and Synthetic Biology II: Analysis and Design of
Cellular Systems, edited by
*,*published by Springer, New York (2014). ISBN: 978-94-017-9046-8 (Print) 978-94-017-9047-5 (Online) DOI 10.1007/978-94-017-9047-5 [PDF] [PDF] Talk: [PDF] [PPT] - Harish
Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan and John H Reif,
Activatable Tiles: Demonstration of Linear and Directed Self Assembly,
abstract, Digital Proceedings of the Ninth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices (FNANO12), Snowbird,
Utah, pp. 109 (April 2012). Also, Sudhanshu Garg, Harish Chandran, Nikhil
Gopalkrishnan, and John Reif, One-Time, Directed and Catalytic Activation
of 1-D DNA Tiles, Poster Abstract DNA19, Tempe, AZ, Sept, 22-27, 2013. Journal
publication: Sudhanshu Garg, Harish Chandran, Nikhil Gopalkrishnan, Thomas
H. LaBean, and John Reif, Directed Enzymatic Activation of 1-D DNA Tiles,
ACS Nano, Volume 9, Issue 2, pages 1072-1079, January 27, 2015. [PDF] [PDF] Supplementary [PDF] DOI: 10.1021/nn504556v
- Hieu Bui, Harish
Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan, Reem Mokhtar, Tianqi
Song and John H Reif, DNA Computing, Chapter in Section 3:
Architecture and Organization, Volume I: Computer Science and Software
Engineering (Edited by
Teofilo F. Gonzalez, Jorge Diaz-Herrera, Allen Tucker), The Computer Science Handbook,
Third Edition (Editor-In-Chief Allen B. Tucker), Taylor & Francis
Group, (2013). ISBN 9781439898529 [PDF]
- Sudhanshu Garg, Nikhil
Gopalkrishnan, Harish Chandran, and John Reif, Self-Replicating DNA
Nanostructures: Autocatalytic Nanodevices derived from Catalytic
Nanodevices, FNANO 2013, Snowbird, Utah, April 15-18, 2013.

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] http://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. Shah S., Song T., Song X., Yang M., Reif J.
(2019) 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 DOI: 10.1007/978-3-030-26807-7_2

273. Xin Song, Shalin Shah,
and John Reif, An Overview of DNA-Based Digital Data Storage, Chapter, DNA- and
RNA-Based Computing Systems (Evgeny Katz, editor), Wiley-VCH Verlag GmbH Publishers, Weinheim,
Germany, to appear (March, 2021).
ISBN10: 3527347208 ISBN13: 9783527347209

274. Reem Mokhtar, Tianqi
Song, Daniel Fu, Shalin Shah, Xin Song, Ming Yang, and John Reif, DNA Origami
Transformers, Chapter, DNA- and RNA-Based Computing Systems (Evgeny Katz,
editor), Wiley-VCH Verlag GmbH
Publishers, Weinheim, Germany, to appear
(March, 2021). ISBN10: 3527347208 ISBN13: 9783527347209 [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 11, Vol 2. Implementations, Alternative
Computing, (edited by Andrew Adamatzky), World Scientific (to appear, 2021). [PDF]

278. Shalin Shah, Ming Yang, Tianqi Song,
and John Reif, Molecular computation via polymerase strand displacement
reactions, Chapter 12, Vol 2. Implementations, Alternative Computing, (edited
by Andrew Adamatzky), World Scientific (to appear, 2021). [PDF]

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).

280. Shah S., Song T.,
Song X., Yang M., Reif J, Implementing Arbitrary CRNs Using Strand Displacing
Polymerase. International Conference on DNA Computing and Molecular Programming
(DNA 2019), Seattle, WA (Aug, 2019). 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]

281. Dan Fu and John H
Reif, Design of Shaped 3D DNA Nanostructures, invited submission to special
issue (Mechanical Design in DNA Nanotechnology) of Applied Sciences,
(2021).

282. Xin Song, Shalin
Shah, John Reif, Multidimensional Data Organization and Random Access in
Large-Scale DNA Storage Systems, invited submission to special issue of Natural
Computing (Theoretical Computer Science – track C), (2021). DIO: https://doi.org/10.1101/743369

283. Xin
Song, Felicity Coulter, Ming Yang, Fikadu Tafesse, William Messer, John Reif, Rapid
At-Home Testing of COVID-19 with an Accurate, Inexpensive, Lyophilized
Molecular Test Kit, manuscript in preparation, April 2021).