Tokyo Institute of Technology

About: Tokyo Institute of Technology is a education organization based out in Tokyo, Tôkyô, Japan. It is known for research contribution in the topics: Catalysis & Thin film. The organization has 46775 authors who have published 101656 publications receiving 2357893 citations. The organization is also known as: Tokyo Tech & Tokodai.

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

Abstract: Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.

Z-Scheme Water Splitting Using Two Different Semiconductor Photocatalysts

Abstract: Water splitting on illuminated semiconductors has long been studied as a potential means of converting solar energy into chemical energy in the form of H2, a clean and renewable energy carrier. Photocatalytic water splitting through two-step photoexcitation using two different semiconductor powders and a reversible donor/acceptor pair (so-called shuttle redox mediator) is one of the possible forms of artificial photosynthesis. This system was inspired by natural photosynthesis in green plants and is called the “Z-scheme”. The development of Z-scheme water splitting systems has relied on both finding a new semiconductor photocatalyst that efficiently works in the presence of a shuttle redox mediator and creating active sites to promote surface chemical reactions while suppressing backward reactions involving redox mediators. This review article describes the historical development of photocatalytic water splitting systems driven by the Z-scheme principle.

Dispersion of fillers and the electrical conductivity of polymer blends filled with carbon black

Abstract: Dispersion state of carbon black(CB) was studied in polymer blends which are incompatible with each other. It was found that CB distributes unevenly in each component of the polymer blend. There are two types of distribution. (1) One is almost predominantly distributed in one phase of the blend matrix, and in this phase fillers are relatively homogeneously distributed in the same manner as a single polymer composite. (2) In the second, the filler distribution concentrates at interface of two polymers. As long as the viscosities of two polymers are comparable, interfacial energy is the main factor determining uneven distribution of fillers in polymer blend matrices. This heterogeneous dispersion of conductive fillers has much effect on the electrical conductivity of CB filled polymer blends. The electrical conductivity of CB filled polymer blends is determined by two factors. One is concentration of CB in the filler rich phase and the other is phase continuity of this phase. These double percolations affect conductivity of conductive particle filled polymer blends.

Photomobile polymer materials: towards light-driven plastic motors.

Abstract: As light is a good energy source that can be controlled remotely, instantly, and precisely, light-driven soft actuators could play an important role for novel applications in wideranging industrial and medical fields. Liquid-crystalline elastomers (LCEs) are unique materials having both properties of liquid crystals (LCs) and elastomers, and a large deformation can be generated in LCEs, such as reversible contraction and expansion, and even bending, by incorporating photochromic molecules, such as an azobenzene, with the aid of photochemical reactions of these chromophores. Herein we demonstrate new sophisticated motions of LCEs and their composite materials: a plastic motor driven only by light. If materials absorb light and change their shape or volume, they can convert light energy directly into mechanical work (the photomechanical effect) and could be very efficient as a single-step energy conversion. Furthermore, these photomobile materials would be widely applicable because they can be controlled remotely just by manipulating the irradiation conditions. LCEs show an anisotropic order of mesogens with a cooperative effect, which leads them to undergo an anisotropic contraction along the alignment direction of mesogens when heated above their LC-isotropic(I) phase transition temperatures (TLC-I) and an expansion by lowering the temperature below TLC-I. [1, 13–18] The expansion and contraction is due to the microscopic change in alignment of mesogens, followed by the significant macroscopic change in order through the cooperative movement of mesogens and polymer segments. It is well known that when azobenzene derivatives are incorporated into LCs, the LC-I phase transition can be induced isothermally by irradiation with UV light to cause trans–cis photoisomerization, and the I-LC reverse-phase transition by irradiation with visible light to cause cis–trans back-isomerization. This photoinduced phase transition (or photoinduced reduction of LC order) has led successfully to a reversible deformation of LCEs containing azobenzene chromophores just by changing the wavelength of actinic light. Although the photoinduced deformation of LCEs previously reported is large and interesting, it is limited to contraction/expansion and bending, preventing them from being used for actual applications. Herein we report potentially applicable rotational motions of azobenzene-containing LCEs and their composite materials, including a first lightdriven plastic motor with laminated films composed of an LCE film and a flexible polyethylene (PE) sheet. The LCE films were prepared by photopolymerization of a mixture of an LC monomer containing an azobenzene moiety (molecule 1 shown in Scheme 1) and an LC diacrylate with an azobenzene moiety (2 in Scheme 1) with a ratio of 20/ 80 mol/mol, containing 2 mol% of a photoinitiator in a glass cell coated with rubbed polyimide alignment layers. The photopolymerization was conducted at a temperature at which the mixture exhibited a smectic phase. The glasstransition temperature of the LCE films is at about room temperature, allowing the LCE films to work at room temperature in air, as the films are flexible enough at this temperature. We prepared a continuous ring of the LCE film by connecting both ends of the film. The azobenzene mesogens were aligned along the circular direction of the ring. Upon exposure to UV light from the downside right and visible light from the upside right simultaneously (Figure 1), the ring

Simultaneous polymerization and formation of polyacetylene film on the surface of concentrated soluble Ziegler-type catalyst solution

Abstract: A direct method of simultaneously polymerizing and forming acetylene monomer to produce uniformly thin films of polyacetylene was investigated in terms of catalyst system, catalyst concentration, and polymerization temperature. The best catalyst was a Ti(OC4H9)4–Al(C2H5)3 system (Al/Ti = 3–4) and the critical concentration was 3 mmole/l. of Ti(OC4H9)4. Below the critical concentration, only a solid or a powder was obtained. The configuration of the polymers obtained depends strongly upon the polymerization temperature. Thus an all-cis polymer was obtained at temperatures lower than −78°C, whereas an all-trans polymer resulted at temperatures higher than 150°C. Observations either in an electron microscope by direct transmission or in a scanning electron microscope showed that the film is composed of an accumulation of fibrils about 200–300 A in width and of indefinite length.