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.

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 Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

2021 ◽  
Author(s):  
Jaeyoung K. Jung ◽  
Khalid K. Alam ◽  
Julius B. Lucks
Keyword(s):  
Response Times ◽  
Dna Nanotechnology ◽  
Fine Tuning ◽  
Digital Converter ◽  
Strand Displacement ◽  
Design Rules ◽  
Analog To Digital ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Molecular Computations

ABSTRACTCell-free biosensors are emerging as powerful platforms for monitoring human and environmental health. Here, we expand the capabilities of biosensors by interfacing their outputs with toehold-mediated strand displacement circuits, a dynamic DNA nanotechnology that enables molecular computation through programmable interactions between nucleic acid strands. We develop design rules for interfacing biosensors with strand displacement circuits, show that these circuits allow fine-tuning of reaction kinetics and faster response times, and demonstrate a circuit that acts like an analog-to-digital converter to create a series of binary outputs that encode the concentration range of the target molecule being detected. We believe this work establishes a pathway to create “smart” diagnostics that use molecular computations to enhance the speed, robustness and utility of biosensors.

Implementing Feedforward Neural Network Using DNA Strand Displacement Reactions

NANO ◽  
2020 ◽  
pp. 2150001
Author(s):  
Siyan Zhu ◽  
Qiang Zhang
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Modular Design ◽  
Reaction Network ◽  
Nonlinear Problems ◽  
Feedforward Neural Network ◽  
Strand Displacement ◽  
Logic Operation ◽  
Dna Strand Displacement ◽  
Dna Strand

The ability of neural networks to process information intelligently has allowed them to be successfully applied in the fields of information processing, controls, engineering, medicine, and economics. The brain-like working mode of a neural network gives it incomparable advantages in solving complex nonlinear problems compared with other methods. In this paper, we propose a feedforward DNA neural network framework based on an enzyme-free, entropy-driven DNA reaction network that uses a modular design. A multiplication gate, an addition gate, a subtraction gate, and a threshold gate module based on the DNA strand displacement principle are cascaded into a single DNA neuron, and the neuron cascade is used to form a feedforward transfer neural network. We use this feedforward neural network to realize XOR logic operation and full adder logic operation, which proves that the molecular neural network system based on DNA strand displacement can carry out complex nonlinear operation and reflects the powerful potential of building these molecular neural networks.

scholarly journals Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

2017 ◽  
Vol 121 (12) ◽  
pp. 2594-2602 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Bernard Yurke ◽  
Elton Graugnard ◽  
William L. Hughes
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Locked Nucleic Acids ◽  
Dna Strand ◽  
Kinetics Of

Biocomputing based on DNA strand displacement reactions

ChemPhysChem ◽  
2021 ◽  
Author(s):  
Hui Lv ◽  
Qian Li ◽  
Jiye Shi ◽  
Fei Wang ◽  
Chunhai Fan
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

scholarly journals Kinetics of Toehold-Mediated DNA Strand Displacement Depend on FeII4L4 Tetrahedron Concentration

Nano Letters ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 1368-1374
Author(s):  
Jinbo Zhu ◽  
Filip Bošković ◽  
Bao-Nguyen T. Nguyen ◽  
Jonathan R. Nitschke ◽  
Ulrich F. Keyser
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Kinetics Of

Highly sensitive multiplex detection of microRNA by competitive DNA strand displacement fluorescence assay

Talanta ◽  
2019 ◽  
Vol 200 ◽  
pp. 487-493 ◽  
Author(s):  
Raja Chinnappan ◽  
Rawa Mohammed ◽  
Ahmed Yaqinuddin ◽  
Khalid Abu-Salah ◽  
Mohammed Zourob
Keyword(s):  
Fluorescence Assay ◽  
Multiplex Detection ◽  
Strand Displacement ◽  
Highly Sensitive ◽  
Dna Strand Displacement ◽  
Dna Strand

Development of DNA computing and information processing based on DNA-strand displacement

2015 ◽  
Vol 58 (10) ◽  
pp. 1515-1523 ◽  
Author(s):  
Yafei Dong ◽  
Chen Dong ◽  
Fei Wan ◽  
Jing Yang ◽  
Cheng Zhang
Keyword(s):  
Information Processing ◽  
Dna Computing ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand
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