Publications [#237052] of John H. Reif

Journal articles or Book chapters PUBLISHED

1. Chandran, H; Gopalkrishnan, N; Phillips, A; Reif, J, Localized hybridization circuits, in International Conference on DNA Computing and Molecular Programming (DNA17), California Institute of Technology, Pasadina, California, Lecture Notes for Computer Science (LNCS), edited by Luca Cardelli and William Shih, Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, vol. 6937 LNCS (September, 2011), pp. 64-83, Springer Berlin Heidelberg, NYC, NY, ISSN 0302-9743 [pdf], [doi]
   (last updated on 2026/01/14)

   Abstract:
   Molecular computing executed via local interactions of spatially contiguous sets of molecules has potential advantages of (i) speed due to increased local concentration of reacting species, (ii) generally sharper switching behavior and higher precision due to single molecule interactions, (iii) parallelism since each circuit operates independently of the others and (iv) modularity and scalability due to the ability to reuse DNA sequences in spatially separated regions. We propose detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates. The circuits act via enzyme-free DNA hybridization reaction cascades. Our designs include composable OR, AND and propagation Boolean gates, and techniques to achieve higher degree fan-in and fan-out. A biophysical model of localized hybridization reactions is used to estimate the effect of locality on reaction rates. We also use the Visual DSD simulation software in conjunction with localized reaction rates to simulate a localized circuit for computing the square root of a four bit number. © 2011 Springer-Verlag.