Pattern Recognition of 2 × 2 Matrices Based on DNA Strand Displacement

2019 ◽  
Vol 11 (10) ◽  
pp. 1357-1365
Author(s):  
Yanfeng Wang ◽  
Aolong LV ◽  
Chun Huang ◽  
Junwei Sun
Keyword(s):  
Pattern Recognition ◽  
Large Scale ◽  
Logic Circuits ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Complex Circuits ◽  
Dna Strand ◽  
Simple Logic

Biochemical circuits have been transformed from simple logic circuits to large-scale complex circuits, benefitting from the maturity of DNA strand displacement technology. Pattern recognition is a process of analyzing perceptual signals and identifying and interpreting objects. In this study, pattern recognition of 2 × 2 matrices based on DNA strand displacement was designed, including dual-rail circuits and seesaw circuits. The effective results were obtained by simulation in Visual DSD software, simultaneously, the pattern recognition and DNA strand displacement technology were perfectly combined.

scholarly journals A programming language for composable DNA circuits

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Andrew Phillips ◽  
Luca Cardelli
Keyword(s):  
Programming Language ◽  
Large Scale ◽  
Implementation Strategies ◽  
Logic Circuits ◽  
Arbitrary System ◽  
Strand Displacement ◽  
Dna Computation ◽  
Simulation Tools ◽  
Dna Strand Displacement ◽  
Dna Strand

Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.

Simple Logic Computation Based on the DNA Strand Displacement

2014 ◽  
Vol 11 (9) ◽  
pp. 1975-1982 ◽  
Author(s):  
Yanfeng Wang ◽  
Guihua Tian ◽  
Hewei Hou ◽  
Mengmeng Ye ◽  
Guangzhao Cui
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Logic Computation ◽  
Dna Strand ◽  
Simple Logic

scholarly journals Molecular computations with competitive neural networks that exploit linear and nonlinear kinetics

10.29007/rfzv ◽  
2018 ◽  
Author(s):  
Anthony J. Genot ◽  
Teruo Fujii ◽  
Yannick Rondelez
Keyword(s):  
Neural Networks ◽  
Pattern Recognition ◽  
Nonlinear Effects ◽  
Molecular Networks ◽  
Strand Displacement ◽  
Nonlinear Kinetics ◽  
Dna Strand Displacement ◽  
Linear And Nonlinear ◽  
Dna Strand ◽  
Molecular Computations

We show how to exploit enzymatic saturation -an ubiquitous nonlinear effects in biochemistry- in order to process information in molecular networks. The networks rely on the linearity of DNA strand displacement and the nonlinearity of enzymatic replication. We propose a pattern-recognition network that is compact and should be robust to leakage.

scholarly journals Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Anupama J. Thubagere ◽  
Chris Thachuk ◽  
Joseph Berleant ◽  
Robert F. Johnson ◽  
Diana A. Ardelean ◽  
...  
Keyword(s):  
Large Scale ◽  
Strand Displacement ◽  
Systematic Construction ◽  
Dna Strand Displacement ◽  
Dna Strand

Functional Analysis of Large-Scale DNA Strand Displacement Circuits

2013 ◽  
pp. 189-203 ◽  
Author(s):  
Boyan Yordanov ◽  
Christoph M. Wintersteiger ◽  
Youssef Hamadi ◽  
Andrew Phillips ◽  
Hillel Kugler
Keyword(s):  
Functional Analysis ◽  
Large Scale ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

Research of Molecule Logic Circuit Based on DNA Strand Displacement Reaction

2016 ◽  
Vol 13 (10) ◽  
pp. 7684-7691 ◽  
Author(s):  
Zicheng Wang ◽  
Zijie Cai ◽  
Zhonghua Sun ◽  
Jian Ai ◽  
Yanfeng Wang ◽  
...  
Keyword(s):  
Logic Circuits ◽  
Logic Circuit ◽  
The Other ◽  
Strand Displacement ◽  
Molecular Logic ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Gold Nanoprobe ◽  
Decoder Circuit ◽  
Strand Displacement Reaction

Because of its outstanding advantages, DNA strand displacement (DSD) reaction has been widely used for signals processing and molecular logic circuit constructing. Two digital logic circuits are constructed in this paper. One is the encoder circuit with four inputs and two outputs, and the other is the decoder circuit with two inputs and four outputs. Of particular interest to us is the multicolor fluorescent gold nanoprobe detection part, where a gold nanoparticle is modified with multicolor fluorophores which exploits the ultrahigh quenching ability of gold nanoparticles (AuNPs). Finally, the circuits can be programmed and simulated with the software Visual DSD. The simulated results based on DSD show that the molecular circuits constructed in this paper is reliable and effective, which has wide prospects in logical circuits and nano-electronics study.

scholarly journals 8-Bit Adder and Subtractor with Domain Label Based on DNA Strand Displacement

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2989 ◽  
Author(s):  
Weixuan Han ◽  
Changjun Zhou
Keyword(s):  
Dna Computing ◽  
Logic Gates ◽  
Logic Circuits ◽  
Calculation Model ◽  
Strand Displacement ◽  
High Concentration ◽  
Low Concentration ◽  
Molecular Logic ◽  
Dna Strand Displacement ◽  
Dna Strand

DNA strand displacement, which plays a fundamental role in DNA computing, has been widely applied to many biological computing problems, including biological logic circuits. However, there are many biological cascade logic circuits with domain labels based on DNA strand displacement that have not yet been designed. Thus, in this paper, cascade 8-bit adder/subtractor with a domain label is designed based on DNA strand displacement; domain t and domain f represent signal 1 and signal 0, respectively, instead of domain t and domain f are applied to representing signal 1 and signal 0 respectively instead of high concentration and low concentration high concentration and low concentration. Basic logic gates, an amplification gate, a fan-out gate and a reporter gate are correspondingly reconstructed as domain label gates. The simulation results of Visual DSD show the feasibility and accuracy of the logic calculation model of the adder/subtractor designed in this paper. It is a useful exploration that may expand the application of the molecular logic circuit.

A DNA Logic Model for Building Large-Scale Circuits Based on DNA Strand Displacement

2018 ◽  
Vol 13 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Zicheng Wang ◽  
Jian Ai ◽  
Yanfeng Wang ◽  
Hongbo Meng ◽  
Guangzhao Cui
Keyword(s):  
Large Scale ◽  
Logic Model ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand
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