Unit Tiles Research Articles

DNA lattice growth with single, double, and triple double-crossover boundaries by stepwise self-assembly

Construction of various nanostructures with nanometre-scale precision through various DNA building blocks depends upon self-assembly, base-pair complementarity and sequence programmability. During annealing, unit tiles are formed by the complementarity of base pairs in each strand. Enhancement of growth of target lattices is expected if seed lattices (i.e. boundaries for growth of target lattices) are initially present in a test tube during annealing. Although most processes for annealing DNA nanostructures adopt a one-step high temperature method, multi-step annealing provides certain advantages such as reusability of unit tiles and tuneability of lattice formation. We can construct target lattices effectively (through multi-step annealing) and efficiently (via boundaries) by multi-step annealing and combining boundaries. Here, we construct efficient boundaries made of single, double, and triple double-crossover DNA tiles for growth of DNA lattices. Two unit double-crossover DNA tile-based lattices and copy-logic implemented algorithmic lattices were introduced to test the growth of target lattices on boundaries. We used multi-step annealing to tune the formation of DNA crystals during fabrication of DNA crystals comprised of boundaries and target lattices. The formation of target DNA lattices was visualized using atomic force microscopy (AFM). The borders between boundaries and lattices in a single crystal were clearly differentiable from AFM images. Our method provides way to construct various types of lattices in a single crystal, which might generate various patterns and enhance the information capacity in a given crystal.

Erosion and redeposition pattern on the W7-X graphite test divertor unit tile

A set of plasma-facing components was retrieved from the W7-X vessel after OP1.2b campaign with an inertially cooled Test Divertor Unit (TDU) and analyzed postmortem to provide data on the plasma-surface interactions processes in the complex device geometry. In the present study, the lower TDU horizontal target (HT) graphite tile HM19TM400hTE2 exposed to the plasma during both OP 1.2 campaigns was examined. The surface modification of the material caused by the plasma-wall interactions was determined. The study employed several microscopy methods including SEM, FIB, STEM, TEM, EDX, and optical profilometry which showed that (i) distinct erosion zone was located at the inner HT strike line position, (ii) the area covered by a pronounced deposit was located adjacent the erosion zone, (iii) the target finger substructures positioned close to the outboard side was unaltered, and (iv) significant changes to surface roughness values along the length of the plate occurred.

Quasicrystal-related mosaics with periodic lattices interlaid with aperiodic tiles.

Quasicrystals, which have long-range orientational order without translational symmetry, are incompatible with the theory of conventional crystals, which are characterized by periodic lattices and uniformly repeated unit cells. Reported here is a novel quasicrystal-related solid state observed in two Al-Cr-Fe-Si alloys, which can be described as a mosaic of aperiodically distributed unit tiles in translationally periodic structural blocks. This new type of material possesses the opposing features of both conventional crystals and quasicrystals, which might trigger wide interest in theory, experiments and the potential applications of this type of material.

Programmable assembly of gold nanoparticle nanoclusters and lattices.

Deterministic assembly of metallic nanoparticles (e.g. gold nanoparticles) into prescribed configurations has promising applications in many fields such as biosensing and drug delivery. DNA-directed bottom-up assembly has demonstrated unparalleled capability to precisely organize metallic nanoparticles into assemblies of designer configurations. However, the fabrication of assemblies comprising delicate nanoparticle arrangements, especially across large dimensions (e.g. micron size), has remained challenging. In this report, we have designed DNA origami hexagon tiles that are capable of assembling into higher-order networks of honeycomb arrays or tubes with dimensions up to several microns. The versatile addressability of the unit tile enables precise and periodic positioning of nanoparticles onto these higher-order DNA origami frame structures. Overall, we have constructed a series of 9 gold nanoparticle architectures with programmable configurations ranging from nanometer-sized clusters to micrometer-sized lattices. We believe these architectures shall hold great application potential in numerous biomedical fields.

Kurt Bruckner’s view on the Penrose tiling

We demonstrate the potential of Kurt Bruckner’s ‘addition algorithm’, which is based on the substitution rule for the generation of the Robinson triangle tiling, a variant of the Penrose tiling. The artist Kurt Bruckner developed his straightforward approach intuitively for the creation of quasiperiodic ornaments. This versatile method can be used for the construction of achiral, homochiral and racemic quasiperiodic ornaments, as well as for the generation of decorated two-level (two-color) Penrose tilings. Therefore, the underlying tiling is always the same kind of Penrose tiling, which is invariant under the action of specific mirror and black/white mirror operations in contrast to unit tiles that are decorated in specific ways. Compared to the underlying classical substitution method the advantage of Kurt Bruckner’s approach is its simplicity and versatility for the creation of decorated tilings. Using a vector graphics editor, large and arbitrarily complex quasiperiodic ornaments can be easily generated manually.

NMR Studies of Artificial Double-Crossover DNA Tiles

This report documents the design and characterization of DNA molecular nanoarchitectures consisting of artificial double crossover DNA tiles with different geometry and chemistry. The Structural characterization of the unit tiles, including normal, biotinylated and hairpin loop structures, are morphologically studied by atomic force microscopy. The specific proton resonance of the individual tiles and their intra/inter nucleotide relationships are verified by proton nuclear magnetic resonance spectroscopy and 2-dimensional correlation spectral studies, respectively. Significant up-field and down-field shifts in the resonance signals of the individual residues at various temperatures are discussed. The results suggest that with artificially designed DNA tiles it is feasible to obtain structural information of the relative base sequences. These tiles were later fabricated into 2D DNA lattice structures for specific applications such as protein arrangement by biotinylated bulged loops or pattern generation using a hairpin structure.

Analysis of a scheme for de-magnified Talbot lithography

The authors describe a photolithographic scheme based on the replication of a periodic transparent mask in a photoresist utilizing the coherent self-imaging Talbot effect. A periodic two-dimensional diffractive structure (or Talbot mask) composed of unit tiles distributed in a square matrix was illuminated by a coherent extreme ultraviolet (EUV) beam from a table top EUV laser. The illumination beam was reflected in a spherical mirror and the Talbot mask was placed in the path of the convergent beam. At designed locations determined by the Talbot distance, reduced replicas of the mask were obtained and used to print the slightly de-magnified copies of the mask on the surface of a photoresist. Experimental results showing the de-magnification effect are in good agreement with the diffraction theory. The limits of the technique are discussed.

Molecular behavior of DNA origami in higher-order self-assembly.

DNA-based self-assembly is a unique method for achieving higher-order molecular architectures made possible by the fact that DNA is a programmable information-coding polymer. In the past decade, two main types of DNA nanostructures have been developed: branch-shaped DNA tiles with small dimensions (commonly up to ∼20 nm) and DNA origami tiles with larger dimensions (up to ∼100 nm). Here we aimed to determine the important factors involved in the assembly of DNA origami superstructures. We constructed a new series of rectangular-shaped DNA origami tiles in which parallel DNA helices are arranged in a zigzag pattern when viewed along the DNA helical axis, a design conceived in order to relax an intrinsic global twist found in the original planar, rectangular origami tiles. Self-associating zigzag tiles were found to form linear arrays in both diagonal directions, while planar tiles showed significant growth in only one direction. Although the series of zigzag tiles were designed to promote two-dimensional array formation, one-dimensional linear arrays and tubular structures were observed instead. We discovered that the dimensional aspect ratio of the origami unit tiles and intertile connection design play important roles in determining the final products, as revealed by atomic force microscopy imaging. This study provides insight into the formation of higher-order structures from self-assembling DNA origami tiles, revealing their unique behavior in comparison with conventional DNA tiles having smaller dimensions.

Hydrogen isotopes retention in JT-60U

Poloidal/toroidal distributions of hydrogen isotopes (H,D) retention on the plasma facing surfaces and side surfaces of carbon tiles used in JT-60U were investigated. The retention of hydrogen isotopes is nearly proportional to the thickness of carbon redeposited layers. The redeposited layers on the inner divertor area retain hydrogen isotopes uniformly with the concentration of ∼0.02 in (H+D)/C, while those on the tile sides shadowed from the plasma ∼0.13 in (H+D)/C. Total hydrogen isotopes retention in the whole divertor area including the baffle plates and dome unit tiles of JT-60U is estimated to be ∼4×1024 atoms assuming that the amount of retained hydrogen isotopes is proportional to the integrated discharge time. Some of the first wall tiles are found to retain significantly large amount of deuterium, which is attributed to the injection of energetic deuterium originating from NBI.

Tetravex is NP-complete

TETRAVEX is a widely played one person computer game in which you are given n2 unit tiles, each edge of which is labelled with a number. The objective is to place each tile within a n by n square such that all neighbouring edges are labelled with an identical number. Unfortunately, playing TETRAVEX is computationally hard. More precisely, we prove that deciding if there is a tiling of the TETRAVEX board given n2 unit tiles is NP-complete. Deciding where to place the tiles is therefore NP-hard. This may help to explain why TETRAVEX is a good puzzle. This result compliments a number of similar results for one person games involving tiling. For example, NP-completeness results have been show for: the offline version of Tetris [1], KPlumber (which involves rotating tiles containing drawings of pipes to make a connected network) [2], and shortest sliding puzzle problems [3]. It raises a number of open questions. For example, is the infinite version Turing-complete? How do we generate TETRAVEX problems which are truly puzzling as random NP-complete problems are often surprising easy to solve? Can we observe phase transition behaviour? What about the complexity of the problem when it is guaranteed to have an unique solution? How do we generate puzzles with unique solutions?

Measurement of deuterium and tritium retentions on the surface of JT-60 divertor tiles by means of nuclear reaction analysis

It is important to measure retentions and depth profiles of deuterium and tritium on plasma facing materials to understand plasma-wall interactions. The nuclear reaction analysis (NRA) has been established using a deuteron beam with an adjustable energy. By means of the NRA, depth profiles of deuterium and tritium on the surface of JT-60 divertor graphite tiles irradiated with DD burning were obtained. The NRA method showed that the average concentrations of the deuterium retained in the surface of two different were 1.3 × 10 16 and 0.3 × 10 16 cm −2. α-particles from the T(d, α)n reaction were measured from a dome unit tile of JT-60U W-shaped divertor and the measured activity of tritium was about 18 kBq/cm 2. The peak energy of the α spectrum obtained with the NRA was about 1.2 MeV. This result implies that energetic tritons were implanted in the divertor graphite tile.

The periodic average structure of particular quasicrystals.

The non-crystallographic symmetry of d-dimensional (dD) quasiperiodic structures is incompatible with lattice periodicity in dD physical space. However, dD quasiperiodic structures can be described as irrational sections of nD (n > d) periodic hypercrystal structures. By appropriate oblique projection of particular hypercrystal structures onto physical space, discrete periodic average structures can be obtained. The boundaries of the projected atomic surfaces give the maximum distance of each atom in a quasiperiodic structure from the vertices of the reference lattice of its average structure. These maximum distances turn out to be smaller than even the shortest atomic bond lengths. The metrics of the average structure of a 3D Ammann tiling, for instance, with edge lengths of the unit tiles equal to the bond lengths in elemental aluminium, correspond almost exactly to the metrics of face-centred-cubic aluminium. This is remarkable since most stable quasicrystals contain aluminium as the main constitutent. The study of the average structure of quasicrystals can be a valuable aid to the elucidation of the geometry of quasicrystal-to-crystal transformations. It can also contribute to the derivation of the physically most relevant Brillouin (Jones) zone.

Compressive Properties of Structural Clay Tile Prisms

Many buildings have been constructed with structural clay tile masonry as either infills, bearing walls, or partitions. Little data are available on the strength and constitutive properties of structural clay tile. The limited historical data and the results of some recent testing of structural clay tile prisms are presented. The current program tested side constructed prisms, or prisms with horizontal cells. Testing was performed at various angles to the bed joint. For loading perpendicular to the bed joint, the prism strength can be conservatively estimated as three-tenths of the unit tile strength. A linear relationship between the modulus of elasticity and the prism strength was also developed. Prisms loaded perpendicular to the bed joint exhibited an abrupt brittle failure, with the strain at peak load averaging 0.0014.