61 research outputs found

    Finite state machines implementation using DNA Techniques

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    Abstract A finite-state machine (FSM) is an abstract mathematical model of computation used to design both computer programs and sequential logic circuits. Considered as an abstract model of computation, the finite state machine is weak; it has less computational power than some other models of computation such as the Turing machine. This paper overview the finite-state automata based on Deoxyribonucleic Acid (DNA). Such automata uses massive parallel processing offered by molecular approach for computation and exhibits a number of advantages over traditional electronic implementations

    DNA multi-bit non-volatile memory and bit-shifting operations using addressable electrode arrays and electric field-induced hybridization.

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    DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (23) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations

    DNA-BASED SELF-ASSEMBLY AND NANOROBOTICS: THEORY AND EXPERIMENTS

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    We study the following fundamental questions in DNA-based self-assembly and nanorobotics: How to control errors in self-assembly? How to construct complex nanoscale objects in simpler ways? How to transport nanoscale objects in programmable manner? Fault tolerance in self-assembly: Fault tolerant self-assembly is important for nanofab-rication and nanocomputing applications. It is desirable to design compact error-resilient schemes that do not result in the increase in the original size of the assemblies. We present a comprehensive theory of compact error-resilient schemes for algorithmic self-assembly in two and three dimensions, and discuss the limitations and capabilities of redundancy based compact error correction schemes. New and powerful self-assembly model: We develop a reversible self-assembly model in which the glue strength between two juxtaposed tiles is a function of the time they have been in neighboring positions. Under our time-dependent glue model, we can rigorously study and demonstrate catalysis and self-replication in the tile assembly. We can assemble thin rectangles of size k × N using O

    Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion

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    Abstract. Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nano-structures, in constructing DNA mechanical devices, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA mechanical devices capable of arbitrarily complex behavior. One prototype system towards this goal can be an autonomous DNA mechanical device capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical design and prototype experimental construction of an autonomous unidirectional DNA walking device moving along a linear track, we present here the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5-color universal Turing machine. Our autonomous nanomechanical device, called an Autonomous DNA Turing Machine (ADTM), is thus capable of universal computation and hence complex translational motion, which we define as universal translational motion.

    Molecular robots guided by prescriptive landscapes

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    Traditional robots rely for their function on computing, to store internal representations of their goals and environment and to coordinate sensing and any actuation of components required in response. Moving robotics to the single-molecule level is possible in principle, but requires facing the limited ability of individual molecules to store complex information and programs. One strategy to overcome this problem is to use systems that can obtain complex behaviour from the interaction of simple robots with their environment. A first step in this direction was the development of DNA walkers, which have developed from being non-autonomous, to being capable of directed but brief motion on one-dimensional tracks. Here we demonstrate that previously developed random walkers—so-called molecular spiders that comprise a streptavidin molecule as an inert ‘body’ and three deoxyribozymes as catalytic ‘legs’—show elementary robotic behaviour when interacting with a precisely defined environment. Single-molecule microscopy observations confirm that such walkers achieve directional movement by sensing and modifying tracks of substrate molecules laid out on a two-dimensional DNA origami landscape. When using appropriately designed DNA origami, the molecular spiders autonomously carry out sequences of actions such as ‘start’, ‘follow’, ‘turn’ and ‘stop’. We anticipate that this strategy will result in more complex robotic behaviour at the molecular level if additional control mechanisms are incorporated. One example might be interactions between multiple molecular robots leading to collective behaviour; another might be the ability to read and transform secondary cues on the DNA origami landscape as a means of implementing Turing-universal algorithmic behaviour

    DNA-based molecular templates and devices

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    DNA-based molecular templates and devices

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    Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems

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    Synthetic biology brings engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription– translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.11Yscopu

    Model Checking Temporal Logic Formulas Using Sticker Automata

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    As an important complex problem, the temporal logic model checking problem is still far from being fully resolved under the circumstance of DNA computing, especially Computation Tree Logic (CTL), Interval Temporal Logic (ITL), and Projection Temporal Logic (PTL), because there is still a lack of approaches for DNA model checking. To address this challenge, a model checking method is proposed for checking the basic formulas in the above three temporal logic types with DNA molecules. First, one-type single-stranded DNA molecules are employed to encode the Finite State Automaton (FSA) model of the given basic formula so that a sticker automaton is obtained. On the other hand, other single-stranded DNA molecules are employed to encode the given system model so that the input strings of the sticker automaton are obtained. Next, a series of biochemical reactions are conducted between the above two types of single-stranded DNA molecules. It can then be decided whether the system satisfies the formula or not. As a result, we have developed a DNA-based approach for checking all the basic formulas of CTL, ITL, and PTL. The simulated results demonstrate the effectiveness of the new method
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