Logical Inference by DNA Strand Algebra

Based on the concept of DNA strand displacement and DNA strand algebra we have developed a method for logical inference which is not based on silicon-based computing. Essentially, it is a paradigm shift from silicon to carbon. In this paper, we have considered the inference mechanism, viz. modus ponens, to draw conclusion from any observed fact. Thus, the present approach to logical inference based on DNA strand algebra is basically an attempt to develop expert system design in the domain of DNA computing. We have illustrated our methodology with respect to the worked out example. Our methodology is very flexible for implementation of different expert system applications.

Download Full-text

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

Science China Chemistry ◽

10.1007/s11426-015-5373-2 ◽

2015 ◽

Vol 58 (10) ◽

pp. 1515-1523 ◽

Cited By ~ 6

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

Download Full-text

Model-Based Design and Control of Distributed DNA-Based Systems by Petri Nets

NANO ◽

10.1142/s179329201650003x ◽

2016 ◽

Vol 11 (01) ◽

pp. 1650003

Author(s):

Rizki Mardian ◽

Kosuke Sekiyama

Keyword(s):

Petri Nets ◽

Design Strategy ◽

Multi Agent Systems ◽

Individual Level ◽

Dna Strand Displacement ◽

In Silico Simulation ◽

Dna Strand ◽

High Level ◽

Silicon Based ◽

And Control

Coordination is an important aspect in developing distributed systems. While in silicon-based agents, i.e., mechanical robotics, designing individual-level behavior that may emerge into one global function is a typical approach to such systems, in DNA-based agents, programming of each individual’s behavior still remains a challenge, as they are based on chemical reactions. These reactions occur immediately after all reactants have been mixed into a solution, which introduces challenges in logical control. In this work, we report a design strategy for coordinated event-driven DNA-based systems by using a Petri Nets model. First, computational primitives based on DNA strand displacement reaction are introduced. Second, their molecular implementation is abstracted by Petri Nets for high-level design. Third, as our main contribution, we propose the model of interacting multi-agent systems based on DNA-only reactions. We verify our design via in silico simulation and show initial experiments of Petri Nets operators. From the obtained results, we argue that our design strategy is feasible for coordinating interaction of distributed DNA-based systems.

Download Full-text

A nanopore interface for high bandwidth DNA computing

10.1101/2021.12.30.474555 ◽

2021 ◽

Author(s):

Karen Zhang ◽

Yuan-Jyue Chen ◽

Kathryn Doroschak ◽

Karin Strauss ◽

Luis Ceze ◽

...

Keyword(s):

Fluorescence Spectroscopy ◽

Single Molecule ◽

Dna Computing ◽

Direct Detection ◽

New Paradigm ◽

Single Molecule Level ◽

Oxford Nanopore ◽

Dna Strand Displacement ◽

Order Of Magnitude ◽

Dna Strand

DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies' MinION device). We show that engineered reporter probes can be detected and classified with high accuracy at the single-molecule level directly from raw nanopore signals using deep learning. We then demonstrate this method's utility in multiplexed detection of clinically relevant microRNA sequences. These results increase DSD output bandwidth by an order of magnitude over what is possible with fluorescence spectroscopy, laying the foundations for a new paradigm in DNA circuit readout and programmable multiplexed molecular diagnostics using portable nanopore devices.

Download Full-text

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

Molecules ◽

10.3390/molecules23112989 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2989 ◽

Cited By ~ 2

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.

Download Full-text

Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b01198 ◽

2017 ◽

Vol 121 (12) ◽

pp. 2594-2602 ◽

Cited By ~ 24

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

Download Full-text

Synchronization of hyper-Lorenz system based on DNA strand Displacement

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2020.3048753 ◽

2021 ◽

pp. 1-1

Author(s):

Zou Chengye ◽

Qiang Zhang ◽

Xiaopeng Wei

Keyword(s):

Lorenz System ◽

Strand Displacement ◽

Dna Strand Displacement ◽

Dna Strand

Download Full-text

Training an asymmetric signal perceptron through reinforcement in an artificial chemistry

Journal of The Royal Society Interface ◽

10.1098/rsif.2013.1100 ◽

2014 ◽

Vol 11 (93) ◽

pp. 20131100 ◽

Cited By ~ 14

Author(s):

Peter Banda ◽

Christof Teuscher ◽

Darko Stefanovic

Keyword(s):

State Of The Art ◽

Chemical Species ◽

Mass Action ◽

Mass Action Kinetics ◽

Dna Strand Displacement ◽

Autonomous Adaptation ◽

Biochemical Systems ◽

Dna Strand ◽

Logic Functions ◽

Application Specific

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. In this paper, we begin addressing these challenges with a novel chemical perceptron that can solve all 14 linearly separable logic functions. The system performs asymmetric chemical arithmetic, learns through reinforcement and supports both Michaelis–Menten as well as mass-action kinetics. To enable cascading of the chemical perceptrons, we introduce thresholds that amplify the outputs. The simplicity of our model makes an actual wet implementation, in particular by DNA-strand displacement, possible.

Download Full-text