J. H. Reif and H. R. Lewis, Symbolic Evaluation and the Global Value Graph



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18, 1994, pp. 383-399. [PostScript] [PDF]

  • V. Pan and J.H. Reif, Generalized Compact Multi-grid, Computers Math Applications, Volume 25, Number 9, p.3-5, May 1993. [PDF]

  • J.H. Reif and J. Storer, A Single-Exponential Upper Bound for Finding Shortest Paths in Three Dimensions. Published in Journal of the ACM(JACM), Vol. 41, No. 5, Sept. 1994, pp. 1013-1019. [PDF]

  • S. Chen and J.H. Reif, 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]

  • J.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]

  • A. Yoshida, J. Rolland and J.H. Reif, and, 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, J. Rolland and A. Yoshida, and J.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, p. 71-82, Aug. 1995. Published as Rolland, J.P., A. Yoshida, L. Davis, and J.H. Reif, High resolution inset head-mounted display, Applied Optics: Optical Technology and Biomedical Optics, 37(19), 4183-4193 (1998). [PDF]

  • S. Gupta, Z. Li, and J.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]

  • J.H. Reif, Parallel Molecular 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]

  • J.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, (ACM Press, New York) 1995, pp.751-761. Revised as Efficient Parallel Factorization and Solution of Structured and Unstructured Linear Systems, to appear in Journal of Computer and System Sciences, 2002. [PostScript] [PDF]

  • S. Gupta, Z. Li, and J.H. Reif, Synthesizing Efficient Out-of-Core Programs for Block Recursive Algorithms using Block-Cyclic Data Distributions. Proceedings of the 1996 International Conference on Parallel Processing, Bloomingdale, IL, Proc. Int'l Conf. Parallel Processing, vol. II, pp 142-149, 1996. August 1996. Published inIEEE Transactions on Parallel and Distributed Systems, Vol. 10, No. 3, March 1999, pp 297-315. [PDF] or [PostScript] [PDF]

  • L. Nyland, J. Prins, A. Goldberg, P. Mills, J.H. Reif, and R. Wagner. A Refinement Methodology for Developing Data-Parallel Applications, Euro-Par'96, Lecture Notes in Computer Science, Springer-Verlag, pp.145-150, 1996.

  • S. Chen and J.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, ISBN 0-8186-7358-3, March 1996. [PDF]

  • J.H. Reif and H. Wang, Nonuniform discretization approximation for Kinodynamic motion planning and its applications, Workshop on Foundations of Robotics, Toulouse, France, July 1996, 97-112. Published in Siam Journal of Computing (SICOMP), Volume 30, No. 1, pages 161-190, (2000). [PostScript] [PDF] or [PostScript]

  • Z. Li, P. H. Mills, and J.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, January 3-6, 1995. Published in Parallel Algorithms and Applications, Vol. 8, pp. 35-59, 1996. [PostScript] [PDF]

  • E. Gelenbe, N.Schmajuk, J. Staddon, and J.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]

  • J.H. Reif, Approximate Complex Polynomial Evaluation in Near Constant Work Per Point. Proc. 29th ACM Symposium on Theory of Computing (STOC'97), May 4-6, El Paso, Texas, 1997, pp. 30-39. Published in Siam Journal of Computing (SICOMP), Vol. 28 Number 6 pp. 2059-2089, 1999. [PostScript] [PDF]

  • J.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 [PDF])

  • J.H. Reif and S. Tate, Fast spatial decomposition and closest pair computation for limited precision input, Tech. Report. #N-96-001, Univ. of North Texas, Dept. of Computer Science (1996). Journal of Algorithmica, Volume 28, Number 3, 2000, pp. 271-287. [PDF] or [PostScript] [PDF]

  • S. Chen and J.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]

  • J.H. Reif and D. Yen, Derivation of Parallel Graph Connectivity Algorithms via Stream Contraction, Duke University Technical Report, 1989.

  • J.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. A postscript version of this paper and figures are at URL: [PostScript] [PDF] and [PostScriptFigures]

  • J.H. Reif, On the Impossibility of Interaction-Free Quantum Sensing for Small I/O Bandwidth, Information and Computation, Jan 2000, pp. 1-20. [PostScript] [PDF]

  • J.H. Reif, Robust, Adaptive and Dynamic Robotic Motion Planning, 19th NSF Design and Manufacturing Grantees Conference, Monterrey, Mexico, Jan 1998. [PostScript] [PDF]

  • J.H. Reif and S. 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. [PostScript] [PDF]

  • J.H. Reif, Paradigms for Biomolecular Computation, First International Conference on Unconventional Models of Computation, Auckland, New Zealand, January 1998. Published in Unconventional Models of Computation, edited by C.S. Calude, J. Casti, and M.J. Dinneen, Springer Publishers, January 1998, pp 72-93. [PostScript] [PDF]

  • J.H. Reif and J. 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, March, 1998. [PDF]. Published as Optimal Encoding of Non-stationary Sources, Special Issue of Information Sciences, Volume 135, pp. 87-105 (2001). [PDF]

  • J.H. Reif and H. 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, pages 49-57, June, 1998. [PostScript] [PDF]

  • J.H. Reif and Z. 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, pages 223-236, Mar. 5-7 1998. Published as The Computational Power of Frictional Mechanical Systems, SIAM Journal of Computing(SICOMP), Vol. 32, No. 6, pp. 1449-1474, (2003). [PDF] or [PDF]. Talk slides: [HTML]

  • A. Gehani and J.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 appeared 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]

  • J.H. Reif, Alternative Computational Models: A Comparison of Biomolecular and Quantum Computation, 18th Invited paper, International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS98), (December, 1998). [PostScript] [PDF]

  • J.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]

  • LaBean, T. H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H. & Seeman, N.C., The construction, analysis, ligation and self-assembly of DNA triple crossover complexes, Journal of American Chemistry Society(JACS) 122, 1848-1860 (2000). [PDF]

  • J.H. Reif, Efficient Quantum Compression, submitted for publication, November, 1999. [PostScript] [PDF]

  • J.H. Reif, Quantum Information Processing: Compression, Coding, and Related Computations, (Jan., 1999) [PostScript] [PDF]

  • John Fischer and John Reif, Nonparametric Multiscale Multimodal Model for Detection/Recognition, Multi-Modality Image Fusion Conference, Rochester, NY, Oct 6-7, 1999. [PDF]

  • Gehani, A., T. H. LaBean, and J.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 E. Winfree and D.K. Gifford, American Mathematical Society, Providence, RI, pp. 233-249, (2000). [PDF] talk slides: [PDF]. Published as an invited paper 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).

  • T. H. LaBean, E. Winfree, and J.H. Reif, Experimental Progress in Computation by Self-Assembly of DNA Tilings, Published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Volume 54, edited by E. Winfree and D.K. Gifford, American Mathematical Society, Providence, RI, pp. 123-140, (2000). [PostScript] [PDF] or [PostScript] and [HTML Lecture]

  • J.H. Reif and Z. Sun. An efficient approximation algorithm for weighted region shortest path problem. In Proceedings of the 4th Workshop on Algorithmic Foundations of Robotics(WAFR2000),Pub. by A. K. Peters Ltd, Hanover, New Hampshire, pages 191-203, Mar. 16-18 2000. [PostScript] [PDF]. Talk slides: [HTML]

  • J.H. Reif and Z. 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, pages 450-461, Brown University, Providence, RI, August 8-10, (2001). Published in Algorithmica, Volume 39, Number 2, pages 127-153, February 2004. [PDF] or [PDF]. Talk slides: [HTML]

  • J.H. Reif and T. 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), 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 slides: [PDF]

  • J.H. Reif, T.H. LaBean, and N.C. Seeman, Challenges and Applications for Self-Assembled DNA Nanostructures, Proc. Sixth International Workshop on DNA-Based Computers, 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, 2001, pp. 173-198. [PostScript] [PDF] talk slides: [PDF] [PPT]

  • C. Mao, LaBean, T.H. Reif, J.H., Seeman, Logical Computation Using Algorithmic Self-Assembly of DNA Triple-Crossover Molecules, Nature, vol. 407, Sept. 28 2000, pp. 493-495; C. Erratum: Nature 408, 750-750(2000). [PDF] or [PDF]

  • J.H. Reif and T. H. LaBean, and N.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 (May, 2001).

  • Z. Sun and J.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, Pub. in volume 2223 of Lecture Notes in Computer Science, pages 160-171, Dec, 2001. [PostScript] [PDF]

  • J. H. Reif, T. 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, pages 231-247, (2002). [PostScript] [PDF] slides: [PDF] [PPT]

  • J. 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]

  • J. H. Reif, The Emergence of the 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]

  • J. H. Reif, Molecular Assembly and Computation: From Theory to Experimental Demonstrations, plenary paper, 29-th International Colloquium on Automata, Languages, and Programming(ICALP), Málaga, Spain (July 8, 2002). Lecture Notes in Computer Science, New York, Volume 2380, pages 1-21, (2002). [PostScript][PDF] slides: [PDF] [PPT]

  • J. 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), pages 22-37. Published in Natural Computing, DNA8 special issue, Vol. 2, p 439-461, (2003). [PDF] or [PostScript][PDF] Talk Slides: [PDF]

  • Dage Liu, John H. Reif, Thomas H. LaBean, DNA Nanotubes, Construction and Characterization of Filaments Composed of TX-tile Lattice. 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), pages 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).[PDF]

  • John H. Reif, DNA Computation - Perspectives: Successes and Challenges, Science, 296: 478-479, April 19, 2002. [PostScript][PDF]

  • Z. Sun and J. H. Reif, On Energy-minimizing Paths on Terrains for a Mobile Robot, 2003 IEEE International Conference on Robotics and Automation(ICRA2003), Taipei, Taiwan, May 12-17, 2003. [PostScript] [PDF]

  • D. Hsu, T. Jiang, J. H. Reif, and Z. Sun, The Bridge Test for Sampling Narrow Passages with Probabilistic Roadmap Planners, 2003 IEEE International Conference on Robotics and Automation(ICRA2003), Taipei, Taiwan, May 12-17, 2003. [PostScript] [PDF]

  • Z. Sun and J. H. Reif, 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 publication in special issue of Theoretical Computer Science, 2004. [PostScript] [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). [PostScript] [PDF]

  • Hao Yan, Liping Feng, Thomas H. LaBean, and John 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 Reif), Abstract in Lecture Notes in Computer Science, Springer-Verlag, New York, (2003). Published in Journal of American Chemistry Society(JACS), Vol. 125, No. 47, pp. 14246-14247, 2003. [PDF] or [PDF]

  • Hao Yan, Sung Ha Park, Liping Feng, John 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 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. [PDF] or [PDF]

  • Liping Feng, Sung Ha Park, John H. Reif, and Hao Yan, A Two State DNA Lattice Actuated by DNA Motors, Angewandte Chemie [International Edition], Vol. 42, pp. 4342-4346, Sept. 2003. [PDF] or [PDF]

  • J. H. Reif and Z. Sun, 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, 2003. [PostScript] [PDF]

  • Tinging Jiang and John H. Reif, Efficient Methods for Stochastic Simulations of Biomolecular Motions, submitted for publication, July, 2003. [PDF]

  • Li, H.; Park, S. H.; Reif, John H.; LaBean, T. H.; Yan, H., DNA-Templated Self-Assembly of Protein and Nanoparticle Linear Arrays, Journal of American Chemistry Society(JACS), Vol. 126, No. 2, pp. 418-419, 2004. [PDF]

  • Thomas H. LaBean, Hao Yan, Sung Ha Park, Liping Feng, Peng Yin, Hanying Li, Sang Jung Ahn, Dage Liu, Xiaoju Guan, and John H. Reif, Overview of New Structures for DNA-Based Nanofabrication and Computation, Invited paper to appear in Information Sciences, 2004. [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, Springer-Verlag, New York, (2004). [PDF] Talk: [PDF] [PPT]

  • Peng Yin, Hao Yan, Xiaoju G. Daniell Andrew J. Turberfield, John H. Reif, A Unidirectional DNA Walker Moving Autonomously Along a Linear Track, Submitted for publication, 2004. Abstract: [PDF] Poster: [PDF] [PPT] [PDF]

  • Peng Yin, Andrew J. Turberfield, 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, Springer-Verlag, New York, (2004). [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, Springer-Verlag, New York, (2004). [PDF] Poster: [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, Poster, Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in Computer Science, Springer-Verlag, New York, (2004). [PDF] Poster: [PDF] [PPT]

  • John H. Reif, DNA-Based Nano-Engineering: DNA and its Enzymes as the Engines of Creation at the Molecular Scale, Invited Talk, Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in Computer Science, Springer-Verlag, New York, (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, Computational Modeling and Simulation of Materials (CIMTEC) Conference, Acireale, Sicily, Italy, May 29-June 4, 2004 [PDF]


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