691 research outputs found
Reflections on Tiles (in Self-Assembly)
We define the Reflexive Tile Assembly Model (RTAM), which is obtained from
the abstract Tile Assembly Model (aTAM) by allowing tiles to reflect across
their horizontal and/or vertical axes. We show that the class of directed
temperature-1 RTAM systems is not computationally universal, which is
conjectured but unproven for the aTAM, and like the aTAM, the RTAM is
computationally universal at temperature 2. We then show that at temperature 1,
when starting from a single tile seed, the RTAM is capable of assembling n x n
squares for n odd using only n tile types, but incapable of assembling n x n
squares for n even. Moreover, we show that n is a lower bound on the number of
tile types needed to assemble n x n squares for n odd in the temperature-1
RTAM. The conjectured lower bound for temperature-1 aTAM systems is 2n-1.
Finally, we give preliminary results toward the classification of which finite
connected shapes in Z^2 can be assembled (strictly or weakly) by a singly
seeded (i.e. seed of size 1) RTAM system, including a complete classification
of which finite connected shapes be strictly assembled by a "mismatch-free"
singly seeded RTAM system.Comment: New results which classify the types of shapes which can
self-assemble in the RTAM have been adde
GP-9s Are Ubiquitous Proteins Unlikely Involved in Olfactory Mediation of Social Organization in the Red Imported Fire Ant, Solenopsis invicta
The red imported fire ant (RIFA), Solenopsis invicta, is an invasive species, accidentally introduced in the United States that can cause painful (sometimes life-threatening) stings to human, pets, and livestock. Their colonies have two social forms: monogyne and polygyne that have a single and multiple functional queens, respectively. A major gene (Gp-9), identified as a putative pheromone-binding protein on the basis of a modest amino acid sequence identity, has been suggested to influence the expression of colony social organization. Monogyne queens are reported to possess only the GP-9B alleles, whereas polygyne queens possess both GP-9B and GP-9b. Thus, both social forms are reported to express GP-9B, with GP-9b being a marker expressed in polygynes but it is absent in monogynes. Here, we report two types of polygyne colonies, one that does not express GP-9b (monogyne-like) and the other expressing both proteins, GP-9B and GP-9b. Given their expression pattern, GP-9s are hemolymph proteins, which are more likely to be involved in the transport of lipids and small ligands within the homocoel. GP-9B existed in two forms, one of them is phosphorylated. The helical-rich content of the protein resembles the secondary structures of a beetle hemolymph protein and moth pheromone-binding proteins. An olfactory role is unlikely given the lack of specific expression in the sensillar lymph. In marked contrast to GP-9s, a chemosensory protein, SinvCSP, is demonstrated to be specifically expressed in the antennae. Within the antennae, expression of SinvCSP is restricted to the last two segments, which are known to house olfactory sensilla
Optimization of supply diversity for the self-assembly of simple objects in two and three dimensions
The field of algorithmic self-assembly is concerned with the design and
analysis of self-assembly systems from a computational perspective, that is,
from the perspective of mathematical problems whose study may give insight into
the natural processes through which elementary objects self-assemble into more
complex ones. One of the main problems of algorithmic self-assembly is the
minimum tile set problem (MTSP), which asks for a collection of types of
elementary objects (called tiles) to be found for the self-assembly of an
object having a pre-established shape. Such a collection is to be as concise as
possible, thus minimizing supply diversity, while satisfying a set of stringent
constraints having to do with the termination and other properties of the
self-assembly process from its tile types. We present a study of what we think
is the first practical approach to MTSP. Our study starts with the introduction
of an evolutionary heuristic to tackle MTSP and includes results from extensive
experimentation with the heuristic on the self-assembly of simple objects in
two and three dimensions. The heuristic we introduce combines classic elements
from the field of evolutionary computation with a problem-specific variant of
Pareto dominance into a multi-objective approach to MTSP.Comment: Minor typos correcte
Random, blocky and alternating ordering in supramolecular polymers of chemically bidisperse monomers
As a first step to understanding the role of molecular or chemical
polydispersity in self-assembly, we put forward a coarse-grained model that
describes the spontaneous formation of quasi-linear polymers in solutions
containing two self-assembling species. Our theoretical framework is based on a
two-component self-assembled Ising model in which the bidispersity is
parameterized in terms of the strengths of the binding free energies that
depend on the monomer species involved in the pairing interaction. Depending
upon the relative values of the binding free energies involved, different
morphologies of assemblies that include both components are formed, exhibiting
paramagnetic-, ferromagnetic- or anti ferromagnetic-like order,i.e., random,
blocky or alternating ordering of the two components in the assemblies.
Analyzing the model for the case of ferromagnetic ordering, which is of most
practical interest, we find that the transition from conditions of minimal
assembly to those characterized by strong polymerization can be described by a
critical concentration that depends on the concentration ratio of the two
species. Interestingly, the distribution of monomers in the assemblies is
different from that in the original distribution, i.e., the ratio of the
concentrations of the two components put into the system. The monomers with a
smaller binding free energy are more abundant in short assemblies and monomers
with a larger binding affinity are more abundant in longer assemblies. Under
certain conditions the two components congregate into separate supramolecular
polymeric species and in that sense phase separate. We find strong deviations
from the expected growth law for supramolecular polymers even for modest
amounts of a second component, provided it is chemically sufficiently distinct
from the main one.Comment: Submitted to Macromolecules, 6 figures. arXiv admin note: substantial
text overlap with arXiv:1111.176
DNA-based Self-Assembly of Chiral Plasmonic Nanostructures with Tailored Optical Response
Surface plasmon resonances generated in metallic nanostructures can be
utilized to tailor electromagnetic fields. The precise spatial arrangement of
such structures can result in surprising optical properties that are not found
in any naturally occurring material. Here, the designed activity emerges from
collective effects of singular components equipped with limited individual
functionality. Top-down fabrication of plasmonic materials with a predesigned
optical response in the visible range by conventional lithographic methods has
remained challenging due to their limited resolution, the complexity of
scaling, and the difficulty to extend these techniques to three-dimensional
architectures. Molecular self-assembly provides an alternative route to create
such materials which is not bound by the above limitations. We demonstrate how
the DNA origami method can be used to produce plasmonic materials with a
tailored optical response at visible wavelengths. Harnessing the assembly power
of 3D DNA origami, we arranged metal nanoparticles with a spatial accuracy of 2
nm into nanoscale helices. The helical structures assemble in solution in a
massively parallel fashion and with near quantitative yields. As a designed
optical response, we generated giant circular dichroism and optical rotary
dispersion in the visible range that originates from the collective
plasmon-plasmon interactions within the nanohelices. We also show that the
optical response can be tuned through the visible spectrum by changing the
composition of the metal nanoparticles. The observed effects are independent of
the direction of the incident light and can be switched by design between left-
and right-handed orientation. Our work demonstrates the production of complex
bulk materials from precisely designed nanoscopic assemblies and highlights the
potential of DNA self-assembly for the fabrication of plasmonic nanostructures.Comment: 5 pages, 4 figure
Vector assembly of colloids on monolayer substrates
The key to spontaneous and directed assembly is to encode the desired assembly information to building blocks in a programmable and efficient way. In computer graphics, raster graphics encodes images on a single-pixel level, conferring fine details at the expense of large file sizes, whereas vector graphics encrypts shape information into vectors that allow small file sizes and operational transformations. Here, we adapt this raster/vector concept to a 2D colloidal system and realize 'vector assembly' by manipulating particles on a colloidal monolayer substrate with optical tweezers. In contrast to raster assembly that assigns optical tweezers to each particle, vector assembly requires a minimal number of optical tweezers that allow operations like chain elongation and shortening. This vector approach enables simple uniform particles to form a vast collection of colloidal arenes and colloidenes, the spontaneous dissociation of which is achieved with precision and stage-by-stage complexity by simply removing the optical tweezers
Placement and orientation of individual DNA shapes on lithographically patterned surfaces
Artificial DNA nanostructures show promise for the organization of functional materials to create nanoelectronic or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter 'staple strands', can display 6-nm-resolution patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in solution and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here we describe the use of electron-beam lithography and dry oxidative etching to create DNA origami-shaped binding sites on technologically useful materials, such as SiO_2 and diamond-like carbon. In buffer with ~ 100 mM MgCl_2, DNA origami bind with high selectivity and good orientation: 70–95% of sites have individual origami aligned with an angular dispersion (±1 s.d.) as low as ±10° (on diamond-like carbon) or ±20° (on SiO_2)
Excitonic AND Logic Gates on DNA Brick Nanobreadboards
A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems
Self-assembly of highly symmetrical, ultrasmall inorganic cages directed by surfactant micelles
Nanometre-sized objects with highly symmetrical, cage-like polyhedral shapes, often with icosahedral symmetry, have recently been assembled from DNA(1-3), RNA(4) or proteins(5,6) for applications in biology and medicine. These achievements relied on advances in the development of programmable self-assembling biological materials(7-10), and on rapidly developing techniques for generating three-dimensional (3D) reconstructions from cryo-electron microscopy images of single particles, which provide high-resolution structural characterization of biological complexes(11-13). Such single-particle 3D reconstruction approaches have not yet been successfully applied to the identification of synthetic inorganic nanomaterials with highly symmetrical cage-like shapes. Here, however, using a combination of cryo-electron microscopy and single-particle 3D reconstruction, we suggest the existence of isolated ultrasmall (less than 10 nm) silica cages ('silicages') with dodecahedral structure. We propose that such highly symmetrical, self-assembled cages form through the arrangement of primary silica clusters in aqueous solutions on the surface of oppositely charged surfactant micelles. This discovery paves the way for nanoscale cages made from silica and other inorganic materials to be used as building blocks for a wide range of advanced functional-materials applications
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