We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.

/pdf/real-time-dna-sequencing-from-single-polymerase-molecules-3o0n2kc430.pdf

Real-Time DNA Sequencing from Single Polymerase Molecules

Shape-engineerable and highly densely packed single-walled carbon nanotubes and their application as super-capacitor electrodes

/pdf/shape-engineerable-and-highly-densely-packed-single-walled-slt8pdoyvz.pdf

It is estimated that the world will need to double its energy supply by 2050. Nanotechnology has opened up new frontiers in materials science and engineering to meet this challenge by creating new materials, particularly carbon nanomaterials, for efficient energy conversion and storage. Comparing to conventional energy materials, carbon nanomaterials possess unique size-/surface-dependent (e.g., morphological, electrical, optical, and mechanical) properties useful for enhancing the energy-conversion and storage performances. During the past 25 years or so, therefore, considerable efforts have been made to utilize the unique properties of carbon nanomaterials, including fullerenes, carbon nanotubes, and graphene, as energy materials, and tremendous progress has been achieved in developing high-performance energy conversion (e.g., solar cells and fuel cells) and storage (e.g., supercapacitors and batteries) devices. This article reviews progress in the research and development of carbon nanomaterials during the past twenty years or so for advanced energy conversion and storage, along with some discussions on challenges and perspectives in this exciting field.

Carbon Nanomaterials for Advanced Energy Conversion and Storage

Pacific Biosciences has developed a method for real-time sequencing of single DNA molecules (Eid et al., 2009), with intrinsic sequencing rates of several bases per second and read lengths into the kilobase range. Conceptually, this sequencing approach is based on eavesdropping on the activity of DNA polymerase carrying out template-directed DNA polymerization. Performed in a highly parallel operational mode, sequential base additions catalyzed by each polymerase are detected with terminal phosphate-linked, fluorescence-labeled nucleotides. This chapter will first outline the principle of this single-molecule, real-time (SMRT) DNA sequencing method, followed by descriptions of its underlying components and typical sequencing run conditions. Two examples are provided which illustrate that, in addition to the DNA sequence, the dynamics of DNA polymerization from each enzyme molecules is directly accessible: the determination of base-specific kinetic parameters from single-molecule sequencing reads, and the characterization of DNA synthesis rate heterogeneities.

Real-time DNA sequencing from single polymerase molecules.

2.3. Ionic Liquids (ILs) 5374 2.4. Complexation Reactions on Oxidized CNTs 5375 2.5. Halogenation 5376 2.6. Cycloaddition Reactions 5377 2.7. Radical Additions 5379 2.8. Nucleophilic Additions 5381 2.9. Electrophilic Additions 5381 2.10. Electrochemical Modifications 5381 2.11. Plasma-Activation 5381 2.12. Mechanochemical Functionalizations 5382 3. Noncovalent Interactions 5382 3.1. Polynuclear Aromatic Compounds 5382 3.2. Interactions with Other Substances 5384 3.3. Interactions with Biomolecules 5385 4. Endohedral Filling 5386 4.1. Encapsulation of Fullerenes 5386 4.2. Encapsulation of Organic Substances 5387 4.3. Encapsulation of Inorganic Substances 5387 5. Decoration of CNTs with Metal Nanoparticles 5388 5.1. Covalent Linkage 5388 5.2. Direct Formation on Defect Sites 5388 5.3. Electroless Deposition 5388 5.4. Electrodeposition 5389 5.5. Chemical Decoration 5390 5.6. Deposition of Nanoparticles onto CNTs 5391 5.7. π-π Stacking and Electrostatic Interactions 5391 6. Concluding Remarks 5392 7. Acknowledgments 5392 8. References 5392

Current progress on the chemical modification of carbon nanotubes.

For semiconductors to work properly, it is necessary to improve their electrical properties by adding small amounts of impurities, such as boron, to the semiconducting material, a process called doping. Until now it has been sufficient to introduce dopant atoms randomly. But as semiconductor devices continue to shrink, they will soon reach a size where fluctuations in dopant atom numbers will begin to influence electrical characteristics: dopant distribution can no longer be assumed to be homogeneous if the distance randomly separating these atoms is on a similar scale to the device itself. Shinada et al. have investigated the role of dopant disorder, using a recently developed single-ion implantation technique to implant dopant ions one-by-one into a fine semiconductor region. The results highlight the improvements in device performance that should be achievable through atomic-scale control of the doping process, and may even enhance the prospects for realizing silicon-based solid-state quantum computers. As the size of semiconductor devices continues to shrink, the normally random distribution of the individual dopant atoms within the semiconductor becomes a critical factor in determining device performance—homogeneity can no longer be assumed1,2,3,4,5. Here we report the fabrication of semiconductor devices in which both the number and position of the dopant atoms are precisely controlled. To achieve this, we make use of a recently developed single-ion implantation technique6,7,8,9, which enables us to implant dopant ions one-by-one into a fine semiconductor region until the desired number is reached. Electrical measurements of the resulting transistors reveal that device-to-device fluctuations in the threshold voltage (Vth; the turn-on voltage of the device) are less for those structures with ordered dopant arrays than for those with conventional random doping. We also find that the devices with ordered dopant arrays exhibit a shift in Vth, relative to the undoped semiconductor, that is twice that for a random dopant distribution (- 0.4 V versus -0.2 V); we attribute this to the uniformity of electrostatic potential in the conducting channel region due to the ordered distribution of dopant atoms. Our results therefore serve to highlight the improvements in device performance that can be achieved through atomic-scale control of the doping process. Furthermore, ordered dopant arrays of this type may enhance the prospects for realizing silicon-based solid-state quantum computers10.

Enhancing semiconductor device performance using ordered dopant arrays

A novel interatomic potential energy function is proposed for condensed systems composed of silicon and oxygen atoms, from SiO2 to Si crystal. The potential function is an extension of the Stillinger-Weber potential, which was originally designed for pure Si systems. All parameters in the potential function were determined based on ab initio molecular orbital calculations of small clusters. Without any adjustment to empirical data, the order of stability of five silica polymorphs is correctly reproduced. This potential realizes a large-scale modeling of SiO2/Si interface structures on average workstation computers.

https://iopscience.iop.org/article/10.1143/JJAP.38.L366/pdf

Novel Interatomic Potential Energy Function for Si, O Mixed Systems

A novel point-arc microwave plasma chemical vapor deposition (CVD) apparatus was employed to grow single-walled carbon nanotubes (SWNTs) on Si substrates coated with a sandwich-like nano-layer structure of 0.7 nm Al2O3 (top)/0.5 nm Fe/5–70 nm Al2O3 by conventional high frequency sputtering. The growth of extremely dense and vertically aligned SWNTs with an almost constant growth rate of 270 µm/h within 40 min at a temperature as low as 600°C was demonstrated for the first time. The volume density of the as-grown SWNT films is as higher as 66 kg/m3.

https://iopscience.iop.org/article/10.1143/JJAP.44.1558/pdf

Low Temperature Synthesis of Extremely Dense and Vertically Aligned Single-Walled Carbon Nanotubes

We propose a new oxidation rate equation for silicon supposing only a diffusion of oxidizing species but not including any rate-limiting step by interfacial reaction. It is supposed that diffusivity is suppressed in a strained oxide region near the ${\mathrm{SiO}}_{2}/\mathrm{Si}$ interface. The expression of a parabolic constant in the new equation is the same as that of the Deal-Grove model, while a linear constant makes a clear distinction with that of the model. The estimated thickness using the new expression is close to 1 nm, which compares well with the thickness of the structural transition layers.

New linear-parabolic rate equation for thermal oxidation of silicon

We report a novel method of one-step direct amination on polycrystalline diamond to produce functionalized surfaces for DNA micropatterning by photolithography. Polycrystalline diamond was exposed to UV irradiation in ammonia gas to generate amine groups directly. After patterning, optical microscopy confirmed that micropatterns covered with an Au mask were regular in size and shape. The regions outside the micropatterns were passivated with fluorine termination by C3F8 plasma, and the chemical changes on the two different surfacesthe amine groups inside the patterned regions by one-step direct amination and fluorine termination outside the patterned regionswere characterized by spatially resolved X-ray photoelectron spectroscopy (XPS). The patterned areas terminated with active amine groups were then immobilized with probe DNA via a bifunctional molecule. The sequence specificity was conducted by hybridizing fluorescently labeled target DNA to both complementary and noncomplementary probe DNA attached in...

Iwao Ohdomari

Papers

Enhancing semiconductor device performance using ordered dopant arrays

Novel Interatomic Potential Energy Function for Si, O Mixed Systems

Low Temperature Synthesis of Extremely Dense and Vertically Aligned Single-Walled Carbon Nanotubes

New linear-parabolic rate equation for thermal oxidation of silicon

DNA Micropatterning on Polycrystalline Diamond via One-Step Direct Amination