Formation Of Two-dimensional Arrays Research Articles

Programmable and Pixelated Solute Concentration Fields Controlled by Three-Dimensionally Networked Microfluidic Source/Sink Arrays.

Membrane-integrated microfluidic platforms have played a pivotal role in understanding natural phenomena coupled with solute concentration gradients at the micro- and nanoscale, enabling on-chip microscopy in well-defined planar concentration fields. However, the standardized two-dimensional fabrication schemes in microfluidics have impeded the realization of more complex and diverse chemical environmental conditions due to the limited possible arrangements of source/sink conditions in a fluidic domain. In this study, we present a microfluidic platform with a three-dimensional microchannel network design, where discretized membranes can be integrated and individually controlled in a two-dimensional array format at any location within the entire quasi-two-dimensional solute concentration field. We elucidate the principles of the device to implement operations of the pixel-like sources/sinks and dynamically programmable control of various long-lasting solute concentration fields. Furthermore, we demonstrate the application of the generated solute concentration fields in manipulating the transport of micrometer or submicrometer particles with a high degree of freedom, surpassing conventionally available solute concentration fields. This work provides an experimental tool for investigating complex systems under high-order chemical environmental conditions, thereby facilitating the extensive development of higher-performance micro- and nanotechnologies.

Dewetted bimetallic AuPd nanostructures on silicon carbide surface: Effect of film thickness and annealing temperature

Bimetallic nanostructures are, nowadays, largely investigated in several technological applications due to the synergistic combination of the properties of the two constituting metallic elements. In this regard, AuPd nanostructures are particularly promising combining the peculiar plasmonic properties of Au and the catalytic characteristics of Pd in nanoscale form. Hence, we report here on a thermal-induced dewetting process of deposited bimetallic AuPd films in order to obtain two-dimensional arrays of AuPd nanostructures on SiC surface. SiC is chosen, here, as wide band-gap model substrate enabling potential applications in optical, sensing, energy fields. In particular, we focus our study on the effect of the thickness of the AuPd film and of the annealing temperature on the characteristics of the AuPd dewetting process and on the morphology of the resulting dewetted nanostructures. We sputter-deposited, on the surface of 4H–SiC substrate, bimetallic AuPd thin films, thickness in the 4.3–48.6 nm range, and we carried out annealing processes increasing the annealing temperature from 573 K to 1173 K. As a result, we observed, by atomic force microscopy, the evolution of the AuPd films dewetting process towards the formation of two-dimensional arrays of AuPd nanostructures. In particular, we observed the sequential steps involved in the dewetting process by increasing the annealing temperature: heterogeneous voids nucleation in the films resulting in holes formation (leaving SiC surface exposed), holes growth by continuous addition of vacancies, holes coalescence and metal film retraction leaving interconnected metallic filaments, and filaments decay into isolated nanostructures. The quantification of the fraction of the AuPd-uncovered surface area (i.e. dewetted area leaving exposed SiC surface) versus the annealing temperature for each AuPd film thickness allowed us to evaluate the dewetting temperature (the temperature at which the dewetting process of the film starts) and its evolution with the film thickness. Then, the quantification of the particles average planar and vertical sizes (and the corresponding aspect ratio) was carried out versus the annealing temperature and film thickness. Finally, the temperature-dependent and thickness-dependent growth mode for the dewetted AuPd nanostructures is proposed.

Nucleic acid–induced dimerization of HIV-1 Gag protein

HIV-1 Gag is a highly flexible multidomain protein that forms the protein lattice of the immature HIV-1 virion. In vitro, it reversibly dimerizes, but in the presence of nucleic acids (NAs), it spontaneously assembles into virus-like particles (VLPs). High-resolution structures have revealed intricate details of the interactions of the capsid (CA) domain of Gag and the flanking spacer peptide SP1 that stabilize VLPs, but much less is known about the assembly pathway and the interactions of the highly flexible NA-binding nucleocapsid (NC) domain. Here, using a novel hybrid fluorescence proximity/sedimentation velocity method in combination with calorimetric analyses, we studied initial binding events by monitoring the sizes and conformations of complexes of Gag with very short oligonucleotides. We observed that high-affinity binding of oligonucleotides induces conformational changes in Gag accompanied by the formation of complexes with a 2:1 Gag/NA stoichiometry. This NA-liganded dimerization mode is distinct from the widely studied dimer interface in the CA domain and from protein interactions arising in the SP1 region and may be mediated by protein-protein interactions localized in the NC domain. The formation of the liganded dimer is strongly enthalpically driven, resulting in higher dimerization affinity than the CA-domain dimer. Both detailed energetic and conformational analyses of different Gag constructs revealed modulatory contributions to NA-induced dimerization from both matrix and CA domains. We hypothesize that allosterically controlled self-association represents the first step of VLP assembly and, in concert with scaffolding along the NA, can seed the formation of two-dimensional arrays near the NA.

Structure, Morphology and Reactivity of Conducting Polymer-Linked Polyoxometallate-Modified Gold Nanoparticles

In the present work, Keggin-type polyoxometallates are utilized as both reducing and protecting agents during fabrication of gold nanoparticles ranging from 5 to 100 nm covered (protected) with monolayer-type films of polyoxometallates (phosphododecamolybdates). Immobilization of phosphomolybdate-modified gold nanoparticles into ultrathin layers of conducting polymer films of poly(3,4- ethylenedioxythiophene), PEDOT and polyaniline, PANI is also described. We pursue here the concept based on multiple formation of two-dimensional arrays and three-dimensional networks composed alternately of conducting polymers linking negatively charged monolayer-type films of phosphomolybdate-protected gold nanostructures performed using a layer-by-layer technique. The morphology of the resulting multilayer network films was determined using transmission electron microscopy (TEM) and their formation and electrochemical properties were examined using cycling voltammetry. Resulting monolayer and multilayer assembles composed of phosphomolybdate-stabilized gold nanoparticles have occurred to be attractive towards electrocatalytic reduction of hydrogen peroxide.

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.

Synthesis and bioconjugation of 2 and 3 nm-diameter gold nanoparticles.

By adjustment of solvent conditions for synthesis, virtually monodisperse 4-mercaptobenzoic acid (p-MBA) monolayer-protected gold nanoparticles, 2 and 3 nm in diameter, were obtained. Large single crystals of the 2 nm particles could be grown from the reaction mixture. Uniformity was also demonstrated by the formation of two-dimensional arrays and by quantitative high-angle annular dark-field scanning transmission electron microscopy. The 2 and 3 nm particles were spontaneously reactive for conjugation with proteins and DNA, and further reaction could be prevented by repassivation with glutathione. Conjugates with antibody Fc fragment could be used to identify TAP-tagged proteins of interest in electron micrographs, through the binding of a pair of particles to the pair of protein A domains in the TAP tag.

Formation of Two-Dimensional Array of Multiwalled Carbon Nanotubes in Polystyrene/Poly(methyl methacrylate) Thin Film

Formation of Two-Dimensional Array of Multiwalled Carbon Nanotubes in Polystyrene/Poly(methyl methacrylate) Thin Film

Two-Dimensional Array Formation of Multi-Cellular Spheroids on Micro-Patterned Polymer Brush Surface

Here, a two-dimensional microarray of ten thousand (100x100) hepatocyte hetero-spheroids, underlaid with endothelial cells, was successfully constructed with a 100 µm spacing in an active area of 20x20 mm on micro-fabricated glass substrates coated with poly(ethylene glycol) (PEG) brushes (Fig. 1). Co-cultivation of hepatocytes with endothelial cells was essential to stabilize hepatocyte viability and liver-specific functions, allowing us to obtain hepatocyte spheroids with a diameter of 100 µm, functioning as a miniaturized liver to secret albumin for at least three weeks. The spheroid array constructed here is highly useful as a platform of TBB and CBB to detect a wide variety of clinically, pharmacologically, and toxicologically active compounds through a cellular physiological response.

Backbone dynamics of membrane proteins in lipid bilayers: the effect of two-dimensional array formation as revealed by site-directed solid-state 13C NMR studies on [3-13C]Ala- and [1-13C]Val-labeled bacteriorhodopsin

We have recorded site-directed solid-state 13C NMR spectra of [3-13C]Ala- and [1-13C]Val-labeled bacteriorhodopsin (bR) as a typical membrane protein in lipid bilayers, to examine the effect of formation of two-dimensional (2D) lattice or array of the proteins toward backbone dynamics, to search the optimum condition to be able to record full 13C NMR signals from whole area of proteins. Well-resolved 13C NMR signals were recorded for monomeric [3-13C]Ala-bR in egg phosphatidylcholine (PC) bilayer at ambient temperature, although several 13C NMR signals from the loops and transmembrane α-helices were still suppressed. This is because monomeric bR reconstituted into egg PC, dimyristoylphosphatidylcholine (DMPC) or dipalmytoylphosphatidylcholine (DPPC) bilayers undergoes conformational fluctuations with frequency in the order of 104–105 Hz at ambient temperature, which is interfered with frequency of magic angle spinning or proton decoupling. It turned out, however, that the 13C NMR signals of purple membrane (PM) were almost fully recovered in gel phase lipids of DMPC or DPPC bilayers at around 0 °C. This finding is interpreted in terms of aggregation of bR in DMPC or DPPC bilayers to 2D hexagonal array in the presence of endogenous lipids at low temperature, resulting in favorable backbone dynamics for 13C NMR observation. It is therefore concluded that [3-13C]Ala-bR reconstituted in egg PC, DMPC or DPPC bilayers at ambient temperature, or [3-13C]Ala- and [1-13C]Val-bR at low temperature gave rise to well-resolved 13C NMR signals, although they are not always completely the same as those of 2D hexagonal lattice from PM.

General Model for Lipid-Mediated Two-Dimensional Array Formation of Membrane Proteins: Application to Bacteriorhodopsin

Based on experimental evidence for 2D array formation of bacteriorhodopsin, we propose a general model for lipid-mediated 2D array formation of membrane proteins in lipid bilayers. The model includes two different lipid species, “annular” lipids and “neutral” lipids, and one protein species. The central assumption of the model is that the annular lipids interact more strongly with the protein than with the neutral lipids. Monte Carlo simulations performed on this model show that 2D arrays of proteins only form when there are annular lipids present. In addition, no arrays form if all of the lipids present are annular lipids. The geometry of the observed arrays is for the most part hexagonal. However, for a certain range of low annular lipid/protein ratios, arrays form that have geometries other than hexagonal. Using the assumption that the hydrocarbon chains of the annular lipids are restricted in motion when close to a protein, we expand the model to include a ground state and an excited state of the annular lipids. The main result from the extended model is that within a certain temperature range, increasing the temperature will lead to larger and more regular protein arrays.

Formation of Two-Dimensional Arrays of InP-Based InGaAs Quantum Dots on Patterned Substrates by Selective Molecular Beam Epitaxy

Two-dimensional (2D) arrays of InP-based In0.53Ga0.47As quantum dots are successfully formed using two different approaches of selective molecular beam epitaxial (MBE) growth. One is to introduce modulations into wire-arrays by growing wires on intentionally mis-oriented mesa-stripes based on our recent study on the effect of mis-orientation on the wire growth. The other is to carry out selective MBE growth on a 2D array of <100>-oriented square-mesa pedestals. Both types of InGaAs dot arrays show fairly strong photoluminescence (PL) and cathodoluminescence (CL) emissions, indicating the reasonably good crystal quality of the dots. Both approaches are found to be useful for constructing highly integrated networks of single electron devices.

Silicon drift photodiode array detectors

Silicon drift photodiodes have been constructed in a two-dimensional array format for the purpose of position sensitive detection. The arrays are dimensioned 4/spl times/4, with pixel size 3 mm /spl times/3 mm, and are intended to be used with discrete-channel readout electronics. This aspect of the design limits the overall array dimension in future prototype versions to approximately 10/spl times/10, but allows for higher total count rates than multiplexed or serial-read arrays. The photodiode arrays use the floating cathode ring design described by others. The design reported here, however, differs in that these devices have been specifically processed to maximize the detection efficiency of visible light. This feature makes these detectors attractive for use in position-sensitive scintillator readout. Measurements are presented using these photodiodes coupled to common scintillator crystals to detect gamma-rays. Measurements are also shown using these photodiodes to directly detect low energy X-rays. Typical room temperature noise (ENC) measured in the prototype arrays is 60 electrons rms.

Formation of Two-dimensional Arrays of Annexin V on Phosphatidylserine-containing Liposomes

Annexins are intracellular proteins which bind to membranes in a Ca 2+-dependent manner and which have been proposed to play regulatory roles in different membrane processes. In the present study, the stoichiometry of the Ca 2+-dependent binding of annexin V to phosphatidylserine molecules incorporated into liposomes was studied by fluorescence spectroscopy. The Ca 2+-dependence of the binding was determined using liposomes made of dioleoylphosphatidylserine (PS) and dioleoylphosphatidylcholine (PC), with a PC/PS molar ratio ranging from 1 to 800. These liposomes were shown to be mostly unilamellar by cryo-electron microscopy. [Ca 2+] 1/2 concentrations required for half-maximal binding of annexin V range from 57 μM at PC/PS=1 up to 96 mM at PC/PS=800. Titration of accessible PS molecules showed that annexin V molecules bind equally well to liposomes of PC/PS ratio ranging from 1 to 400. The stoichiometry of the binding between annexin V and PS, determined at low PS content, is eight annexin V molecules per one PS molecule. We propose a novel model of the Ca 2+-dependent interaction between annexin V and lipid membranes, based on the formation of two-dimensional arrays of annexin V molecules, stabilized by both protein-lipid and protein-protein interactions.

Formation of two-dimensional structures from colloidal particles on fluorinated oil substrate

We propose a new type of liquid substrate, perfluorinated oil (F-oil), for the formation of two-dimensional arrays from colloidal particles. The appropriate conditions for particle ordering (experimental cell, type and concentration of surfactants, etc.) are reported. Large and well ordered structures from µm-sized latex particles are obtained. Ordered clusters of globular protein (ferritin) macromolecules are also observed. The structures formed are directly transferred (after the F-oil evaporation) onto a solid substrate for subsequent study by means of optical and electron microscopy. The mechanism of the ordering process is studied and the advantages and disadvantages of the liquid substrates (in comparison with the solid ones) are discussed. Some possible ways for control of the ordering process and for improvement of the quality of the arrays are pointed out.

Energetical and Force Approaches to the Capillary Interactions between Particles Attached to a Liquid-Fluid Interface

Theoretical expressions are derived for calculating the capillary meniscus interactions between two vertical cylinders or two spheres partially immersed in a liquid layer. In general, the radii and the contact angles of the two particles can be different. Two alternative approaches are followed. The first one consists in calculation of capillary interaction energy, which is then differentiated to get the force. In the second approach the force is determined directly by integrating the pressure and the interfacial tension. A very good coincidence between the numerical results of these two independent approaches is established. The results can contribute to a better understanding of phenomena like surface aggregation, surface coagulation, and formation of two-dimensional arrays at interfaces.

Efficient mapping algorithms for a class of hierarchical systems

Proposes techniques for mapping application algorithms onto a class of hierarchically structured parallel computing systems. Multiprocessors of this type are capable of efficiently solving a variety of scientific problems because they can efficiently implement both local and global operations for data in a two-dimensional array format. Among the set of candidate application domains, low-level and intermediate-level image processing and computer vision (IPCV) are characterized by high-performance requirements. Emphasis is given to IPCV algorithms. The importance of the mapping techniques stems from the fact that the current technology cannot be used to build cost-effective and efficient systems composed of very large numbers of processors, so the performance of various systems of lower cost should be investigated. Both analytical and simulation results prove the effectiveness and efficiency of the proposed mapping techniques. >

Analysis of Vertical Cavity Surface Emitting Semiconductor Lasers

We investigate AlGaAs vertical cavity surface emitting lasers for optical excitation and current modulation. The epitaxial Bragg reflectors of the lasers have a reflectivity of larger than 98.9%. For optical excitation the threshold power is 18 mW and the one-sided differential quantum efficiency 33%. Single longitudinal and transversal mode emission is observed up to 10 mW cw output power. Current modulation if shown to be a efficient as optical excitation. The devices are well suited for two-dimensional array formation

Novel crystalline sheets of Na,K-ATPase induced by phospholipase A2

Treatment of purified preparations of Na,K-ATPase by phospholipase A2 has led to the formation of two-dimensional crystals of the protein. Control tests with another phospholipase and two detergents have shown that crystallization occurs as the result of hydrolysis and/or solubilization of the phospholipids in the enzyme vesicles. Experimentation with various buffer systems has indicated that reduction in the amount of phospholipids alone is sufficient for inducing the formation of crystalline sheets. Inclusion of crystal inducing ions in the buffer facilitates the crystallization process, resulting in more extensive arrays. The new crystalline sheets are exclusively dimeric with average unit cell dimensions:a = 15.8 ± 0.4nm, b = 4.9 ± 0.2nm, and γ = 64 ± 3°. Examination of the micrographs shows that the initial intermolecular interaction leading to the formation of sheets is between the α subunits. Results from this study suggest that removal and/or modification of phospholipids by phospholipases could prove successful in crystallizing those membrane proteins in which excess lipid is the main barrier to the formation of two-dimensional arrays.

High-affinity and low-affinity vanadate binding to sarcoplasmic reticulum Ca 2+-ATPase labeled with fluorescein isothiocyanate

Conditions were found that allowed both the fluorescence detection of vanadate binding to the Ca 2+-ATPase of skeletal muscle sarcoplasmic reticulum and the vanadate-induced formation of two-dimensional arrays of the enzyme. The fluorescence intensity of fluorescein isothiocyanate-labeled Ca 2+-ATPase increased with high-affinity vanadate binding ( K a = 10 6 M −1 ) as reported by Pick and Karlish (Pick, U. and Karlish, S.D. (1982) J. Biol. Chem. 257, 6120–6126). The Ca 2+ and Mg 2+ dependencies for high-affinity vanadate binding were similar but not identical to those for orthophosphate. In addition, it was found that there is low-affinity ( K a = 380 M −1 ) vanadate binding, which causes a 25% decrease in fluorescence. The Ca 2+ and Mg 2+ dependencies of the low-affinity vanadate binding were different from those of orthophosphate or high-affinity vanadate binding. The covalent attachment of fluorescein isothiocyanate (FITC) in the ATP site of the Ca 2+-ATPase did not affect the formation of two-dimensional arrays, as detected by negatively stained electron micrographs. Vanadate concentrations high enough to saturate the low-affinity binding caused two-dimensional arrays as reported by Dux and Martonosi (Dux, L. and Martonosi, A. (1983) J. Biol. Chem. 258, 2599–2603). In addition, freeze-fracture replicas of quick-frozen specimens showed rows of indentations in the inner leaflet of the bilayer that corresponds to the arrays seen on the outer leaflet. This appearance of indentations suggests that low-affinity vanadate binding causes a transmembrane movement of the Ca 2+-ATPase. By contrast, high-affinity vanadate binding was shown to cause neither array formation nor the appearance of indentations.

Electron microscopic evidence for the transmembrane displacement of calcium ATPase.

Incubation of the Ca2+-ATPase in vanadate solutions leads to the formation of two-dimensional arrays in the sarcoplasmic reticulum membrane. Electron micrographic freeze fracture replicas show depressions on the inner leaflet for the first time. This indicates that the ATPase has moved perpendicular to the plane of the membrane. Our results also suggest that aggregation of the Ca2+-ATPase into the two-dimensional arrays occurs before they move into the membrane. These phenomena were observed as soon as 15 minutes after vanadate was added. The effects of vanadate appear to be completely reversible. When SR was incubated in the vanadate solutions and was then diluted into a buffer containing Ca2+ and ATP, the ATPase activity was normal for up to several hours of incubation and only somewhat reduced after 3 days.