Logic circuits based on molecular spider systems

Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity.

[1]  Gerhard A Blab,et al.  Time-dependent motor properties of multipedal molecular spiders. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[2]  Erwin Frey,et al.  Cooperative effects enhance the transport properties of molecular spider teams , 2013 .

[3]  Matthew R. Lakin,et al.  Scalable Design of Logic Circuits Using an Active Molecular Spider System , 2015, IPCAT.

[4]  D. Stefanovic,et al.  Exercises in Molecular Computing , 2014, Accounts of chemical research.

[5]  Matthew R. Lakin,et al.  Supervised Learning in an Adaptive DNA Strand Displacement Circuit , 2015, DNA.

[6]  Darko Stefanovic,et al.  The Effects of Multivalency and Kinetics in Nanoscale Search by Molecular Spiders , 2014, Evolution, Complexity and Artificial Life.

[7]  Jonathan Bath,et al.  A DNA-based molecular motor that can navigate a network of tracks. , 2012, Nature nanotechnology.

[8]  Matthew R. Lakin,et al.  Catalytic Molecular Logic Devices by DNAzyme Displacement , 2014, Chembiochem : a European journal of chemical biology.

[9]  Chris Thachuk,et al.  DNA Walker Circuits: Computational Potential, Design, and Verification , 2013, DNA.

[10]  Darko Stefanovic,et al.  Multivalent Random Walkers - A Model for Deoxyribozyme Walkers , 2011, DNA.

[11]  Darko Stefanovic,et al.  Chemistry at a Higher Level of Abstraction , 2011 .

[12]  Erik Winfree,et al.  Molecular robots guided by prescriptive landscapes , 2010, Nature.

[13]  Darko Stefanovic,et al.  Catalytic Molecular Walkers: Aspects of Product Release , 2013, ECAL.

[14]  Ruojie Sha,et al.  A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.

[15]  Andrew Phillips,et al.  Localized Hybridization Circuits , 2011, DNA.

[16]  Luis Ceze,et al.  DNA-based molecular architecture with spatially localized components , 2013, ISCA.

[17]  Darko Stefanovic,et al.  Behavior of polycatalytic assemblies in a substrate-displaying matrix. , 2006, Journal of the American Chemical Society.

[18]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[19]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[20]  Darko Stefanovic,et al.  Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. , 2006, Biochemistry.

[21]  Tibor Antal,et al.  Molecular spiders with memory. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[22]  Darko Stefanovic,et al.  Cooperative linear cargo transport with molecular spiders , 2012, Natural Computing.

[23]  David Mohr,et al.  First-passage properties of molecular spiders. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[24]  N. Seeman,et al.  A precisely controlled DNA biped walking device , 2004 .

[25]  N. Pierce,et al.  A synthetic DNA walker for molecular transport. , 2004, Journal of the American Chemical Society.

[26]  N. Seeman,et al.  A Proximity-Based Programmable DNA Nanoscale Assembly Line , 2010, Nature.

[27]  Darko Stefanovic,et al.  Superdiffusive transport by multivalent molecular walkers moving under load. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[28]  Wenyan Liu,et al.  Hierarchical self assembly of patterns from the Robinson tilings: DNA tile design in an enhanced Tile Assembly Model , 2011, Natural Computing.

[29]  Darko Stefanovic,et al.  Maze Exploration with Molecular-Scale Walkers , 2012, TPNC.

[30]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[31]  Darko Stefanovic,et al.  Mechanism of diffusive transport in molecular spider models. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[32]  Darko Stefanovic,et al.  Deoxyribozyme-based logic gates. , 2002, Journal of the American Chemical Society.

[33]  Darko Stefanovic,et al.  Multiple Molecular Spiders with a Single Localized Source - The One-Dimensional Case - (Extended Abstract) , 2011, DNA.