Design and Simulation of Self-repairing DNA Lattices

Majumder, Urmi; Sahu, Sudheer; LaBean, Thomas H.; Reif, John H.

doi:10.1007/11925903_15

Cited by 12 publications

(5 citation statements)

References 23 publications

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“…Unfortunately, this technique increases the tile set size by a multiplicative factor. Majumder et al [27] proposes a compact self-healing tile set capable of repairing any damage to computations which are reversible. In this paper, however, we are concerned with the extent of repair without any change in design.…”

Section: Self-repair Modelmentioning

confidence: 99%

Probabilistic models for damage and self-repair in DNA self-assembly

Majumder

2010

Molecular Simulation

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To date, research on DNA self-assembly-based nanostructures has mostly been on one-time assembly. However, DNA nanostructures are very fragile and prone to damage. Knowing the extent of damage that can occur under various physical conditions can be useful in designing robust self-assembled nanostructures. This paper presents simple models for estimating the extent of damage in DNA nanostructures due to various external forces, with emphasis on mechanical and thermal forces. We note that these models have not been validated against experimental data. As such, they are only meant to serve as a basis for designing DNA nanostructures that are robust to external damage. We conclude with a discussion on computing the probability of repair of a damaged nanostructure assuming no change in the design of the self-assembling components.

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Section: Self-repair Modelmentioning

confidence: 99%

Probabilistic models for damage and self-repair in DNA self-assembly

Majumder

2010

Molecular Simulation

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“…Thus, a major concern while engineering such systems is the embedding of effective fault tolerant architectures within these designs. Indeed, such architectures have been intensively studied in connection to various dynamical nanosystems, such as for DNA-tile assemblies [32], [33], for fault-tolerant designs for nanowire-based programable logic arrays [34], or for reliable nanoelectronics [35]. During this section, we introduce a fault-tolerant technique for CNFET circuits, and analyze its effect over the reliability of the generated circuits.…”

Section: Fault Tolerant Designs Of Cnt Circuitsmentioning

confidence: 99%

Fault Tolerant Design and Analysis of Carbon Nanotube Circuits Affixed on DNA Origami Tiles

Czeizler

Orponen

2015

IEEE Trans. Nanotechnology

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Due to its programmable nature, DNA nanotechnology is currently one of the most advanced and most reliable self-assembly based methodology for constructing molecular-scale structures and devices. This makes DNA nanotechnologys a highly promising candidate for generating radically new manufacturing technologies. Our specific interest is in the use of DNA as a template and scaffold for the self-assembly of Carbon-Nanotube Field Effect Transistor (CNFET) circuits. In this research we introduced a novel high-level design framework for self-assembling CNFET circuits. According to this methodology, the elements of the circuits, i.e., CNFETs and the connecting carbon nanotube wires, are affixed on different rectangular DNA scaffolds, called tiles, and self-assemble into the desired circuit. The introduced methodology presents several advantages, both at the design level, and for analyzing the reliability of these systems. We make use of these advantages and introduce a new fault-tolerant architecture for CNFET circuits. Then, we analyze its reliability both by computer simulations and by analytical methods.

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“…The conversion of an original error-prone tile set into a new tile set has been proposed in [2] by utilizing healing. In this case, many tiles are removed from the assembly using a corrective process generally referred to as puncturing [12] [15]. The process of puncturing a DNA self-assembly can be thought as equivalent to repair in VLSI chips.…”

Section: Introductionmentioning

confidence: 99%

A Metric for Assessing the Error Tolerance of Tile Sets for Punctured DNA Self-Assemblies

Hashempour

Arani

Lombardi

2008

26th IEEE VLSI Test Symposium (Vts 2008)

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This paper presents a novel metric by which the effectiveness of punctures (as corrective action for error tolerance) can be assessed with respect to tile sets for DNA selfassembly in nano-manufacturing. Initially, the conditions for correct binding of a tile to an existing aggregate are analyzed using a Markovian approach; based on this analysis, it is proved that correct aggregation (as identified with a so-called Ideal Tile Set) is not always met for existing tile sets for nano-manufacturing. Hence, a metric is proposed for assessing tile sets by utilizing punctures. Tile sets are investigated and assessed with respect to features such error (mismatched tile) movement, punctured area and bond types. Subsequently, it is shown that the proposed metric can comprehensively assess the effectiveness of a type of a puncture for a tile set and its capability to attain error tolerance for the desired pattern. Extensive simulation results are provided.

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Design and Simulation of Self-repairing DNA Lattices

Cited by 12 publications

References 23 publications

Probabilistic models for damage and self-repair in DNA self-assembly

Probabilistic models for damage and self-repair in DNA self-assembly

Fault Tolerant Design and Analysis of Carbon Nanotube Circuits Affixed on DNA Origami Tiles

A Metric for Assessing the Error Tolerance of Tile Sets for Punctured DNA Self-Assemblies

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