Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks

Farfel, Joseph; Stefanović, Darko

doi:10.1007/11753681_4

Cited by 8 publications

(18 citation statements)

References 41 publications

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“…Such reports refer to multiple steps on one sample being carried out simultaneously or in a step wise fusion. Continuous or online assays for different samples are referenced far less [15], [16], [17], [18], [19], [20], [21], [22], [23]. The reason for this is that most systems lack an efficient method to exchange samples, thus this becomes the bottleneck in the application.…”

Section: The Modularized Dna Computer Based On Biochipsmentioning

confidence: 96%

A proposed modularized DNA computer, based on biochips

Zhu

Ding

et al. 2009

Proceedings of the First ACM/SIGEVO Summit on Genetic and Evolutionary Computation

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There are limits to miniaturization with current computer technologies. Information-processing capabilities of organic molecules such as DNA can be used in computers to replace digital switching modality. However, without the emergence of microfluidic devices, all operations in vitro would be user regulated. A more advanced model is where robotic and electronic regulation is combined with DNA computing allowing the majority of the operations within the test environment to be carried out automatically. Microfluidics offers the promise of a "lab on a chip" system. This can control pico liter scale volumes, with integrated support for operations such as mixing, storage, PCR, heating/cooling, cell lysis, electrophoresis, and others [1], [2]], [3]. Thus has emerged a vision for creating a hybrid DNA computer: that can use microfluidics for the control paths and biological primitives for computation (the Arithmetic Logical Units). This paper presents a proposed modularized DNA biochip computer that works in accordance with Von Neumann's principles [4]. The biochips are divided into several modules, which have different functions. Thus, biochemical operations can be regulated in a step wise fusion. We then describe each module within the biochip and simulate how the classic Hamiltonian Path Problem would be solved in the proposed DNA computer.

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Section: The Modularized Dna Computer Based On Biochipsmentioning

confidence: 96%

A proposed modularized DNA computer, based on biochips

Zhu

Ding

et al. 2009

Proceedings of the First ACM/SIGEVO Summit on Genetic and Evolutionary Computation

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“…To perturb the reservoir we encode the time-varying input as fluctuations in the influx of species to the reactor. In [2,23], a network of three deoxyribozyme NOT gates showed stable oscillatory dynamics in an open microfluidic reactor. We extend this work by designing a reservoir computer using deoxyribozyme-based oscillators and investigating their information-processing capabilities.…”

Section: Reservoir Computing Using Deoxyribozyme Oscillatorsmentioning

confidence: 99%

“…However, this model is mathematically unwieldy. We first reduce the oscillator ODEs in [2] to a form more amenable to mathematical analysis: indicate chemical concentration and should not be confused with the matrix notation introduced above. When explicitly talking about the concentrations at time t, we use P i (t) and S i (t).…”

Section: Reservoir Computing Using Deoxyribozyme Oscillatorsmentioning

confidence: 99%

“…In our system, we achieve this by fluctuating inside the reactor are zero. Two of the product concentrations P 2 (0) and P 3 (0) are also set to zero, but to break the symmetry in the system and let the oscillation begin we set Figure 3 shows the traces of computer simulation of this model, where τ = 30 s. We use the reaction rate constant from [2], β = 5 × 10 −7 nM s −1 . Although the kinetics of immobilized deoxyribozyme may be different, for simplicity we use the reaction rate constant of free deoxyribozymes and we assume that we can find deoxyribozymes with appropriate kinetics when immobilized.…”

Section: Reservoir Computing Using Deoxyribozyme Oscillatorsmentioning

confidence: 99%

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DNA Reservoir Computing: A Novel Molecular Computing Approach

Goudarzi

Lakin

Stefanović

2013

Lecture Notes in Computer Science

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Abstract. We propose a novel molecular computing approach based on reservoir computing. In reservoir computing, a dynamical core, called a reservoir, is perturbed with an external input signal while a readout layer maps the reservoir dynamics to a target output. Computation takes place as a transformation from the input space to a high-dimensional spatiotemporal feature space created by the transient dynamics of the reservoir. The readout layer then combines these features to produce the target output. We show that coupled deoxyribozyme oscillators can act as the reservoir. We show that despite using only three coupled oscillators, a molecular reservoir computer could achieve 90% accuracy on a benchmark temporal problem.

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“…For example, a 20-variable 3-SAT problem required 96 hours to complete [1], not counting the considerable time needed for setup and evaluation. To automate and optimize this process, researchers have turned to microfluidic devices [2][3][4][5][6][7][8][9][10]. Microfluidics offers the promise of a "lab on a chip" system that can individually control picoliter-scale quantities of fluids, with integrated support for operations such as mixing, storage, PCR, heating/cooling, cell lysis, electrophoresis, and others [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Abstraction Layers for Scalable Microfluidic Biocomputers

Thies¹,

Urbanski

Thorsen

et al. 2006

DNA Computing

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Abstract. Microfluidic devices are emerging as an attractive technology for automatically orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been integrated on a single chip, and recent trends indicate that the hardware complexity is increasing at rates comparable to Moore's Law. As in the case of silicon, it will be critical to develop abstraction layers-such as programming languages and Instruction Set Architectures (ISAs)-that decouple software development from changes in the underlying device technology. Towards this end, this paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers. A novel algorithm translates microfluidic mixing operations from the BioStream layer to the Fluidic ISA. To demonstrate the benefits of these abstraction layers, we build two microfluidic chips that can both execute BioStream code despite significant differences at the device level. We consider this to be an important step towards building scalable biological computers.

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Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks

Cited by 8 publications

References 41 publications

A proposed modularized DNA computer, based on biochips

A proposed modularized DNA computer, based on biochips

DNA Reservoir Computing: A Novel Molecular Computing Approach

Abstraction Layers for Scalable Microfluidic Biocomputers

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