Abstract: Interfacing of single photon emitters, such as quantum dots, with photonic nanocavities enables study of fundamental quantum electrodynamic phenomena. In such experiments, the inability to precisely position quantum emitters at the nanoscale usually limits the ability to control spontaneous emission, despite sophisticated control of optical density of states by cavity design. Thus, effective light-matter interactions in photonic nanostructures strongly depend on deterministic positioning of quantum emitters. In this work by using directed self-assembly of DNA origami we demonstrate deterministic coupling of quantum dots with gallium phosphide (GaP) dielectric whispering gallery mode resonators design to enhance CdSe quantum dot emission at 600nm-650nm. GaP microdisk and microring resonators are dry-etched through 200nm layer of gallium phosphide on silicon dioxide/silicon substrates. Our simulations show that such GaP resonators may have quality factors up to 10^5, which ensures strong light-matter interaction. On the top surface of microresonators, we write binding sites in the shape of DNA origami using electron beam lithography, and use oxygen plasma exposure to chemically activate these binding sites. DNA origami self-assembly is accomplished by placing DNA origami – quantum dot complexes into these binding sites. This approach allows us to achieve deterministic placement of the quantum dots with a few nm precision in position relative to the resonator. We will report photoluminescence spectroscopy and lifetime measurements of quantum dot – resonator deterministic coupling to probe the cavity-enhanced spontaneous emission rate. Overall, this approach offers precise control of emitter positioning in nanophotonic structures, which is a critical step for scalable quantum information processing.

No.: 9919
ID: CaltechAUTHORS:20180706-090357843

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Abstract: The specificity of Watson-Crick base-pairing allows great control over the design and synthesis of artificial DNA nanostructures. Periodic one-dimensional (1D) tubes, 2D lattices, and 3D crystals are easily created from “DNA tiles” with spacings of 10-20 nanometers. “DNA origami” allows the folding of long DNA strands into arbitrary shapes and patterns up to about 100 nanometers in size with five nanometer features. This suggests that DNA self-assembly might be used for sublithographic fabrication of devices or even circuits. There are, however, a number of challenges. For example, compared to the inorganic materials used as semiconductors, DNA has poor electronic properties and must be augmented by other materials. Such challenges must be solved before DNA self-assembly can be used in a complete process for nanofabrication. We will present partial solutions to a few of them.

ID: CaltechAUTHORS:20130409-135916746

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Abstract: My acquaintance with Ned Seeman began in the Caltech library sometime during 1992. At the time, I was trying to design a DNA computer and was collecting papers in an attempt to learn all the biochemical tricks ever performed with DNA. Among the papers was Ned and Junghuei Chen's beautiful construction of a DNA cube [2]. I had no idea how to harness such a marvel for computation - the diagrams explaining the cube were in a visual language that I could not parse and its static structure, once formed, did not seem to allow further information processing. However, I was in awe of the cube and wondered what kind of mad and twisted genius had conjured it.

Publication: Nanotechnology: Science and Computation
ID: CaltechAUTHORS:20111021-092409943

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Abstract: Self-assembly is a process in which basic units aggregate under attractive forces to form larger compound structures. Recent theoretical work has shown that pseudo-crystalline self-assembly can be algorithmic, in the sense that complex logic can be programmed into the growth process [26]. This theoretical work builds on the theory of two-dimensional tilings [8], using rigid square tiles called Wang tiles [24] for the basic units of self-assembly, and leads to Turing-universal models such as the Tile Assembly Model [28]. Using the Tile Assembly Model, we show how algorithmic self-assembly can be exploited for fabrication tasks such as constructing the patterns that define certain digital circuits, including demultiplexers, RAM arrays, pseudowavelet transforms, and Hadamard transforms. Since DNA self-assembly appears to be promising for implementing the arbitrary Wang tiles [30, 13] needed for programming in the Tile Assembly Model, algorithmic self-assembly methods such as those presented in this paper may eventually become a viable method of arranging molecular electronic components [18], such as carbon nanotubes [10, 1], into molecular-scale circuits.

No.: 2943
ID: CaltechAUTHORS:20110309-104202667

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Abstract: Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes. It has been suggested that intricate self-assembly processes will ultimately be used in circuit fabrication, nano-robotics, DNA computation, and amorphous computing. In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18]. The first is the Minimum Tile Set Problem, where the goal is to find the smallest tile system that uniquely produces a given shape. The second is the Tile Concentrations Problem, where the goal is to decide on the relative concentrations of different types of tiles so that a tile system assembles as quickly as possible. The first problem is akin to finding optimum program size, and the second to finding optimum running time for a "program" to assemble the shape.Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes. It has been suggested that intricate self-assembly processes will ultimately be used in circuit fabrication, nano-robotics, DNA computation, and amorphous computing. In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18]. The first is the Minimum Tile Set Problem, where the goal is to find the smallest tile system that uniquely produces a given shape. The second is the Tile Concentrations Problem, where the goal is to decide on the relative concentrations of different types of tiles so that a tile system assembles as quickly as possible. The first problem is akin to finding optimum program size, and the second to finding optimum running time for a "program" to assemble the shape. We prove that the first problem is NP-complete in general, and polynomial time solvable on trees and squares. In order to prove that the problem is in NP, we present a polynomial time algorithm to verify whether a given tile system uniquely produces a given shape. This algorithm is analogous to a program verifier for traditional computational systems, and may well be of independent interest. For the second problem, we present a polynomial time $O(\log n)$-approximation algorithm that works for a large class of tile systems that we call partial order systems.

ID: CaltechAUTHORS:ADLstoc02

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Abstract: Molecular self-assembly gives rise to a great diversity of complex forms, from crystals and DNA helices to microtubules and holoenzymes. We study a formal model of pseudocrystalline self-assembly, called the Tile Assembly Model, in which a tile may be added to the growing object when the total interaction strength with its neighbors exceeds a parameter Τ. This model has been shown to be Turing-universal. Thus, self-assembled objects can be studied from the point of view of computational complexity. Here, we define the program size complexity of an NxN square to be the minimum number of distinct tiles required to self-assemble the square and no other objects. We study this complexity under the Tile Assembly Model and find a dramatic decrease in complexity, from N^2 tiles to O(log N) tiles, as Τ is increased from 1 (where bonding is noncooperative) to 2 (allowing cooperative bonding). Further, we find that the size of the largest square uniquely produced by a set of n tiles grows faster than any computable function.

ID: CaltechAUTHORS:20161213-162052032

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Abstract: Bacteria employ restriction enzymes to cut or restrict DNA at or near specific words in a unique way. Many restriction enzymes cut the two strands of double-stranded DNA at different positions leaving overhangs of single-stranded DNA. Two pieces of DNA may be rejoined or ligated if their terminal overhangs are complementary. Using these operations fragments of DNA, or oligonucleotides, may be inserted and deleted from a circular piece of plasmid DNA. We propose an encoding for the transition table of a Turing machine in DNA oligonucleotides and a corresponding series of restrictions and ligations of those oligonucleotides that, when performed on circular DNA encoding an instantaneous description of a Turing machine, simulate the operation of the Turing machine encoded in those oligonucleotides. DNA based Turing machines have been proposed by Charles Bennett but they invoke imaginary enzymes to perform the state-symbol transitions. Our approach differs in that every operation can be performed using commercially available restriction enzymes and ligases.

No.: 27
ID: CaltechAUTHORS:20111024-134806267

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