An Efficient Framework for Scalable Defect Isolation in Large Scale Networks of DNA Self-Assembly

This paper proposes and evaluates an approach for defect isolation of DNA self-assembled networks made of a large number of processing nodes. The complexity of DNA self-assembled networks makes impractical to add a large amount of redundancy and employ inefficient and unscalable defect tolerant schemes. A previous framework based on a broadcast algorithm isolates defective nodes without incorporating redundancy for nodes. However, its disadvantage is the limited scalability, thus making it unsuitable for extremely large scale networks built by DNA self-assembly. The proposed framework improves upon the previous framework by involving three algorithmic tiers; namely, 1-hop wave expansion, efficient via placement, and unsafe node detection. The performance of the proposed framework is evaluated and compared with the original framework by considering large scale networks (up to 2,000 × 2,000 nodes), and a novel gross defect model (as well as a conventional random defect model as assumed in previous works). Simulation results indicate that the proposed framework outperforms the original framework in broadcast latency and efficiency and shows excellent scalability for DNA self-assembled nano-scale networks.

Measurement of far-infrared optical constants by ATR

Using an optically-pumped far-infrared laser as a light source, the far-infrared optical constants of liquid acetonitrile, methanol, dichloromethane, and chlorobenzene were obtained by measuring the attenuated total reflections of light for two mutually perpendicular polarizations. The ATR prism of hyper-pure silicon was made asymmetric to avoid the effect of the multiple reflection inside the prism.     

Gold nanoparticle-induced formation of artificial protein capsids

Gold nanoparticles are generally considered to be biologically inactive. However, in this study we show that the addition of 1.4 nm diameter gold nanoparticle induces the remodeling of the ring-shaped protein TRAP into a hollow, capsid-like configuration. This structural remodeling is dependent upon the presence of cysteine residues on the TRAP surface as well as the specific type of gold nanoparticle. The results reveal an apparent novel catalytic role of gold nanoparticles.     

Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis

An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Upon applying a voltage, the DNA hairpin migrated slowly compared to a random sequence ssDNA in the presence of the PNA probe. This retardation was induced by strand invasion of the PNA into the DNA hairpin to form a hybridized complex, where the PEG segment received a large amount of hydrodynamic friction during electrophoresis. The binding constant between the PNA probe and the DNA hairpin was easily determined by mobility analysis. This simple method would be potentially beneficial in studying binding behaviors of various artificial nucleotides to natural DNA or RNA.     

Young’s Modulus and Poisson’s Ratio Changes in Japanese Radish and Carrot Root Tissues during Boiling

Young’s modulus and Poisson’s ratio changes in Japanese radish and carrot during boiling were examined. Young’s modulus decreased rapidly within 2 min, then the decrease moderated. Carrot (3.0 to 0.5 MPa) exhibited increased modulus values relative to radish (1.8 to 0.3 MPa) during the same boiling period. Poisson’s ratio decreased slightly during boiling; carrot Poisson’s ratio (0.40 to 0.33) was smaller than radish (0.35 to 0.23) during the same boiling period. Boiling in saline solutions increased moduli reductions under the same treatment conditions. These results indicated that carrot maintained hardness, but reduced volume relative to radish during boiling.     

Aerobic Methane Oxidation Coupled to Denitrification: Kinetics and Effect of Oxygen Supply

Aerobic methane oxidation coupled to denitrification (AME-D) is a process in which aerobic methanotrophs oxidize methane and release organic compounds that are used by coexisting denitrifiers as electron donors for denitrification. This process is potentially promising for denitrification of wastewater or landfill leachate poor in organic carbon using methane produced onsite as external electron donor. We studied the kinetics of an aerobic methane-oxidizing denitrifying culture and investigated the effect of dissolved oxygen (DO) concentration and air supply rate on AME-D using a batch reactor and a semicontinuous reactor setup. At methane concentrations of 18–33% in air and air flow rates of 15–35?mL?air?L?1?liquid?min?1, the DO concentration was less than 0.01?mg?L?1 and the nitrate removal reached a maximum value of 56.7?mg?NO3–N?g?1?VSS?d?1 with 79% being attributed to denitrification. When the air supply rate was increased to 70?mL?air?L?1?liquid?min?1 resulting in a drop in methane content to 10%, the DO concentration in the bioreactor rose to about 0.8–1.0?mg?L?1 and the total nitrate removal dropped to about 10?mg?NO3–N?g?1?VSS?d?1 with none of it being attributed to denitrification.     

Quantification of the effects of organic and carbonate buffers on arsenate and phosphate adsorption on a goethite-based granular porous adsorbent

Interest in the development of oxide-based materials for arsenate removal has led to a variety of experimental methods and conditions for determining arsenate adsorption isotherms, which hinders comparative evaluation of their adsorptive capacities. Here, we systematically investigate the effects of buffer (HEPES or carbonate), adsorbent dose, and solution pH on arsenate and phosphate adsorption isotherms for a previously well characterized goethite-based adsorbent (Bayoxide E33 (E33)). All adsorption isotherms obtained at different adsorbate/adsorbent concentrations were identical when 1 mM of HEPES (96 mg C/L) was used as a buffer. At low aqueous arsenate and phosphate concentration (～1.3 μM), however, adsorption isotherms obtained using 10 mM of NaHCO(3) buffer, which is a reasonable carbonate concentration in groundwater, are significantly different from those obtained without buffer or with HEPES. The carbonate competitive effects were analyzed using the extended triple layer model (ETLM) with the adsorption equilibrium constant of carbonate calibrated using independent published carbonate adsorption data for pure goethite taking into consideration the different surface properties. The successful ETLM calculations of arsenate adsorption isotherms for E33 under various conditions allowed quantitative comparison of the arsenate adsorption capacity between E33 and other major adsorbents initially tested under varied experimental conditions in the literature.     

Intercomparison of irradiance measurements based on WRR and ETL irradiance scales

We report the corrected intercomparison of the World Radiometer Reference (WRR) irradiance scale and the Electrotechnical Laboratory (ETL) spectral irradiance scale. In addition, we confirm the intercomparison precision using the test facility where the irradiance of ETL 500 W standard lamp can be measured directly with the cavity radiometer. The results showed that the irradiance based on the WRR scale was 0.5–0.7% lower than the one based on the ETL scale.