http://www.cis.udel.edu/~dna3 or email to dna3-inquiry@cis.udel.edu

PROGRAM

3rd DIMACS Workshop on DNA Based Computers

• June 22, Sunday, the day before the meeting.
  AFTERNOON: Two Tutorials, 1pm Computer Science and 3pm Biolab Techniques.
  
  
• June 23, Monday, the first day of the meeting.
  MORNING: Making it work in the Lab, Part 1. Chaired by Leonard Adleman.
  • 9:00 "Physical Chemistry of Nucleic Acid Hybridization"
    James G. Wetmur (Invited paper)
  • 9:45 "Thermodynamic Simulation of Deoxyoligonucleotide Hybridization for DNA Computation"
    Alexander J. Hartemink, David K. Gifford
  • 10:15 Coffee Break
  • 11:00 "The Efficiency of Sequence-Specific Separation of DNA Mixtures for Biological Computing"
    Julia Khodor, David K. Gifford
  • 11:30 "The Effect of Uniform Melting Temperatures on the Efficiency of DNA Computing"
    J.A. Rose, R. Deaton, M. Garzon, S.E. Stevens Jr.
  • 12:00 "A New DNA Separation Technique with Low Error Rate"
    Junghuei Chen, David Wood
  
  
• June 23, Monday, the first day of the meeting.
  AFTERNOON: Proposed Applications. Chaired by Erik Winfree.
  • 2:00 "DNA 2 DNA Computations: A Potential `Killer App'?"
    Laura F. Landweber, Richard Lipton (Invited paper)
  • 2:45 "New Directions in Nucleic Acid Computing: Selected Ribozymes that Can Implement Re-Write Rules"
    Michael P.Robertson, Andrew D. Ellington
  • 3:15 Coffee Break
  • 4:00 "A Surface-Based DNA Algorithm for Minimal Set Cover"
    Tony L. Eng, Benjamin M. Serridge
  • 4:30 "Solid Phase DNA Solution to the Hamiltonian Path Problem"
    Nobuhiko Morimoto, Masanori Arita Akira Suyama
  • 5:00 "Molecular Approximation Algorithm for NP Optimization Problems"
    Richard Beigel, Bin Fu
  
  EVENING: 5:30 pm to 7:00 pm RECEPTION
  
  
• June 24, Tuesday, the second day of the meeting.
  MORNING: Making it work in the Lab, Part 2. Chaired by Nadrian Seeman.
  • 8:30 "Towards Parallel Evaluation and Learning of Boolean mu-Formulas with Molecules"
    Masami Hagiya, Masanori Arita (Invited paper)
  • 9:15 "Wet Splicing Systems"
    Elizabeth Laun, Kalluru J. Reddy
  • 9:45 Coffee Break
  • 10:30 "Parallel Overlap Assembly of Paths Through a Directed Graph"
    Peter Kaplan, David Thaler, Albert Libchaber
  • 11:00 "Parallel Primer Extension Horizontal Chain Reactions as a Paradigm of Parallel DNA-Based Computation"
    Martin Orlian, Frank Guarnieri, Carter Bancroft
  • 11:30 "Bit Operations Using a DNA Template"
    Thomas H. Leete, Joshua Klein, Jerome S. Salem, Harvey Rubin
  
  
• June 24, Tuesday, the second day of the meeting.
  AFTERNOON: Proposed Algorithmic Approaches. Chaired by Richard Lipton.
  • 1:30 "Protein Folding, Spin Glass and Computational Complexity"
    Aviezri Fraenkel (Invited paper)
  • 2:15 "Creating 3-Dimensional Graph Structures with DNA"
    Natasha Jonoska, Stephen A. Karl, Masahico Saito
  • 2:45 Coffee Break
  • 3:30 "DNA Implementation of Nondeterminism"
    Y. Gao, M. Garzon, R.C. Murphy, J.A. Rose, R. Deaton, D.R. Franceschetti, S.E. Stevens Jr.
  • 4:00 "Arithmetic and Logic Operations with DNA"
    Vineet Gupta, Srinivasan Parthasarathy, Mohammed J. Zaki
  
  AFTERNOON: Poster Session.
  • "On Error-Correcting Structures Derived from DNA"
    Myron Deputat, George Hajduczok, Erich Schmitt
  • "On the Encoding Problem for DNA Computing"
    M. Garzon, R. Deaton, P. Neathery, R.C. Murphy, D.R. Franceschetti, S.E. Stevens Jr.
  • "DNA Computing at Surfaces: 4 Base Mismatch Word Design"
    Anthony G. Frutos, Andrew J. Thiel, Anne E. Condon, Lloyd M. Smith, Robert M. Corn
  • "Surface-Based DNA Computation: Hybridization and Destruction"
    Qinghua Liu, Andrew J. Thiel, Anthony G. Frutos, Robert M. Corn, Lloyd M. Smith
  • "In Vitro Selection and Characterization of DNA Enzymes"
    Dirk Faulhammer, Michael Famulok
  
  AFTERNOON: Impromptu Posters and Brief Impromptu Presentations
  (Reserve through dna3-inquiry@cis.udel.edu.)
  
  EVENING: 6:30 pm to 7:15 pm RECEPTION, and 7:15 pm to 9:30 pm DINNER
  
  
• June 25, Wednesday, the third day of the meeting.
  MORNING: Models of DNA Computers. Chaired by Lila Kari.
  • 9:00 "Local Parallel Biomolecular Computation"
    John H. Reif (Invited paper)
  • 9:45 "DNA-Based Parallel Computation by `Counting'"
    Mitsunori Ogihara, Animesh Ray
  • 10:15 Coffee Break
  • 11:00 "Parallel Computation on a DNA Substrate"
    Andrew J. Blumberg
  • 11:30 "Design for a DNA Conformational Processor"
    Michael Conrad, Klaus-Peter Zauner
  • 12:00 "Linear DNA Self-Assembly with Hairpins Generates the Equivalent of Linear Context-Free Grammars"
    Tony Eng
  
  
• June 25, Wednesday, the third day of the meeting.
  AFTERNOON: Computability Using DNA. Chaired by John Reif.
  • 1:30 "Watson-Crick Finite Automata"
    Rudolf Freund, Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa (Invited paper)
  • 2:15 "At the Crossroads of DNA Computing and Formal Languages: Characterizing Recursively Enumerable Languages Using Insertion-Deletion Systems"
    Lila Kari, Gheorghe Paun, Gabriel Thierrin, Sheng Yu
  • 2:45 Coffee Break
  • 3:30 "DNA-EC: A Model of DNA-Computing Based on Equality Checking"
    Takashi Yokomori, Satoshi Kobayashi
  • 4:00 "Splicing on Tree-like Structures"
    Yasubumi Sakakibara, Claudio Ferretti