Graphical classification of DNA sequences of HLA alleles by deep learning.

Alleles of human leukocyte antigen (HLA)-A DNAs are classified and expressed graphically by using artificial intelligence "Deep Learning (Stacked autoencoder)". Nucleotide sequence data corresponding to the length of 822 bp, collected from the Immuno Polymorphism Database, were compressed to 2-dimensional representation and were plotted. Profiles of the two-dimensional plots indicate that the alleles can be classified as clusters are formed.

Classification of C2C12 cells at differentiation by convolutional neural network of deep learning using phase contrast images.

In the field of regenerative medicine, tremendous numbers of cells are necessary for tissue/organ regeneration. Today automatic cell-culturing system has been developed. The next step is constructing a non-invasive method to monitor the conditions of cells automatically.

Fabrication of nanobeads from nanocups by controlling scission/crosslinking in organic polymer materials.

The development of several kinds of micro/nanofabrication techniques has resulted in many innovations in the micro/nanodevices that support today's science and technology. With feature miniaturization, the fabrication tools have shifted from light to ionizing radiation. Here, we propose a simple micro/nanofabrication technique for organic materials using a scanning beam (SB) of ionizing radiation.

Formation and decay of fluorobenzene radical anions affected by their isomeric structures and the number of fluorine atoms.

Aryl fluoride has attracted much attention as a resist component for extreme ultraviolet (EUV) lithography, because of the high absorption cross section of fluorine for EUV photons; however, less is known about electron attachment to fluorobenzene (FBz) and the stability of the reduced state. Picosecond and nanosecond pulse radiolysis of tetrahydrofuran solutions of FBz from mono-, di-, tri-, tetra-, penta-, and hexafluorobenzene was performed, and the effects of isomeric structure and number of fluorine atoms were examined. Scavenging of solvated electrons was found to correlate with the electron affinity obtained by density functional theory in the gas phase, whereas the decay of FBz radical anions was dominated by the activation energy of fluorine anion dissociation calculated using a polarized continuum model (PCM).

"Bicontinuous cubic" liquid crystalline materials from discotic molecules: a special effect of paraffinic side chains with ionic liquid pendants.

Triphenylene (TP) derivatives bearing appropriate paraffinic side chains with imidazolium ion-based ionic liquid (IL) pendants were unveiled to display a phase diagram with liquid crystalline (LC) mesophases of bicontinuous cubic (Cub(bi)) and hexagonal columnar (Col(h)) geometries. While their phase transition behaviors are highly dependent on the length of the side chains and the size of the ionic liquid pendants, TPs with hexadecyl side chains exclusively form a Cub(bi) LC assembly over an extremely wide temperature range of approximately 200 degrees C from room temperature when the anions of the IL pendants are relatively small. Wide-angle X-ray diffraction analysis suggested that the Cub(bi) LC mesophase contains pi-stacked columnar TP arrays with a plane-to-plane separation of approximately 3.

Ambipolar-transporting coaxial nanotubes with a tailored molecular graphene-fullerene heterojunction.

Despite a large steric bulk of C(60), a molecular graphene with a covalently linked C(60) pendant [hexabenzocoronene (HBC)-C(60); 1] self-assembles into a coaxial nanotube whose wall consists of a graphite-like pi-stacked HBC array, whereas the nanotube surface is fully covered by a molecular layer of clustering C(60). Because of this explicit coaxial configuration, the nanotube exhibits an ambipolar character in the field-effect transistor output [hole mobility (micro(h)) = 9.7 x 10(-7) cm(2) V(-1) s(-1); electron mobility (micro(e)) = 1.

Electron transfer processes in subunit I mutants of cytochrome bo quinol oxidase in Escherichia coli.

Cytochrome bo is a terminal quinol oxidase in the aerobic respiratory chain of Escherichia coli. Subunit I binds all four redox centers, and electrons are transferred from quinols to high-spin heme o and Cu(B) through a bound uniquinone-8 and low-spin heme b. To explore the role of conserved charged amino acid residues, we examined the one-electron transfer processes in subunit I mutants.

Conformational relaxation of sigma-conjugated polymer radical anion on picosecond scale.

We report the conformational relaxation of poly[bis(p-n-butylphenyl)silane] (PBPS) radical anion measured by near-ultraviolet-enhanced picosecond pulse radiolysis in tetrahydrofuran solutions. The peak shift and increase in optical density of the transient photoabsorption spectra were investigated by kinetic analysis including reactions of PBPS with solvated/presolvated electrons, peak extraction protocol, and diffusion theory, demonstrating the correspondence in the rate constant (5+/-1x10(2) ps) between the peak shift and increase in oscillator strength. The results were examined by density functional theory and molecular dynamics simulations, where the modeled oligosilane radical anion shows more planner conformation relative to its neutral state and a relaxation time of 8 ps.

Long-lived hole stabilized at a triphenylamine core and shielded by rigid phenylazomethine dendrons: a pulse radiolysis study.

The optical properties and reactivity of one-electron oxidized states (radical cations) of dendrimers are investigated in benzonitrile solutions by nanosecond pulse radiolysis. The hole stabilized at the triphenylamine (TPA) core is effectively shielded by a rigid dendritic phenylazomethine (DPA) shell of four generations, leading to an extension of its lifetime by nearly 2 orders of magnitude in comparison with a core radical cation without dendrons. A continuous red shift of the peak in the photoabsorption spectrum in the visible region and a decrease in the extinction coefficients (oscillator strengths) are found with increasing dendrimer generation number.

Unusual side-chain effects on charge-carrier lifetime in discotic liquid crystals.

When hexa-peri-hexabenzocoronene (HBC) carries paraffinic side chains with ester-ether termini (1a-1c), a hexagonal columnar liquid-crystalline (LC) mesophase forms, which is characterized by a very wide temperature range (ca. 0-300 degrees C). The LC materials from these HBC derivatives show characteristic electronic properties with an extremely long photocarrier lifetime.

Intramolecular electron transfer processes in Cu(B)-deficient cytochrome bo studied by pulse radiolysis.

The Escherichia coli cytochrome bo is a heme-copper terminal ubiquinol oxidase, and functions as a redox-driven proton pump. We applied pulse radiolysis technique for studying the one-electron reduction processes in the Cu(B)-deficient mutant, His333Ala. We found that the Cu(B) deficiency suppressed the heme b-to-heme o electron transfer two order of the magnitude (4.

Anisotropic electron transport properties in sumanene crystal.

The high electron mobility with large anisotropy was attained in the needle-like single crystal of sumanene, which was indicated by time-resolved microwave conductivity (TRMC) measurement.

Function of a bound ubiquinone in Escherichia coli quinoprotein glucose dehydrogenase.

Membrane-bound glucose dehydrogenase (mGDH) is a single integral protein in the respiratory chain in Escherichia coli which oxidizes D-glucose and feeds electrons to ubiquinol oxidase via bulk ubiquinone (UQ). mGDH contains a bound UQ, CoQ8, for its intramolecular electron transfer in addition to pyrroloquinoline quinone (PQQ) as a coenzyme. Pulse radiolysis analysis revealed that the bound UQ exists very close to PQQ at a distance of 11-13 angstroms.

Formation of spectral intermediate G-C and A-T anion complex in duplex DNA studied by pulse radiolysis.

The dynamics of electron adducts of 2'-deoxynucleotides and oligonucelotides (ODNs) were measured spectroscopically by nanosecond pulse radiolysis. The radical anions of the nucleotides were produced within 10 ns by the reaction of hydrated electrons (e(aq)(-)) and were protonated to form the corresponding neutral radicals. At pH 7.

Prominent electron transport property observed for triply fused metalloporphyrin dimer: directed columnar liquid crystalline assembly by amphiphilic molecular design.

A triply fused copper porphyrin dimer, when site-specifically modified on its periphery with hydrophobic and hydrophilic wedges (1C12/TEG), self-assembles into a columnar liquid crystalline (LC) mesophase over a wide-temperature range from -17 to 99 degrees C but gives rise to an amorphous solid when modified with only hydrophobic (1C12/C12) or hydrophilic wedges (1TEG/TEG). A LC film of 1C12/TEG displays at 16 degrees C a top-class one-dimensional electron mobility (0.27 cm2/V x s), as evaluated from its maximum flash-photolysis time-resolved microwave conductivity.

Menaquinone as well as ubiquinone as a bound quinone crucial for catalytic activity and intramolecular electron transfer in Escherichia coli membrane-bound glucose dehydrogenase.

Escherichia coli membrane-bound glucose dehydrogenase (mGDH), which is one of quinoproteins containing pyrroloquinoline quinone (PQQ) as a coenzyme, is a good model for elucidating the function of bound quinone inside primary dehydrogenases in respiratory chains. Enzymatic analysis of purified mGDH from cells defective in synthesis of ubiquinone (UQ) and/or menaquinone (MQ) revealed that Q-free mGDH has very low levels of activity of glucose dehydrogenase and UQ2 reductase compared with those of UQ-bearing mGDH, and both activities were significantly increased by reconstitution with UQ1. On the other hand, MQ-bearing mGDH retains both catalytic abilities at the same levels as those of UQ-bearing mGDH.

Effect of base sequence and deprotonation of Guanine cation radical in DNA.

The deprotonation of guanine cation radical (G+*) in oligonucleotides (ODNs) was measured spectroscopically by nanosecond pulse radiolysis. The G+* in ODN, produced by oxidation with SO4-*, deprotonates to form the neutral G radical (G(-H)*). In experiments using 5-substituted cytosine-modified ODN, substitution of the cytosine C5 hydrogen by a methyl group increased the rate constant of deprotonation, whereas replacement by bromine decreased the rate constant.

Formation of intramolecular poly(4-hydroxystyrene) dimer radical cation.

Poly(4-hydroxystyrene) (PHS) has been used in lithography as a backbone polymer and is also a promising material for extreme-ultraviolet or electron beam lithography. The dynamics of PHS radical cations generated upon exposure to electron beam were investigated. The transient absorption of PHS was observed in the near-infrared region in p-dioxane solutions by pulse radiolysis.

Amphiphilic molecular design as a rational strategy for tailoring bicontinuous electron donor and acceptor arrays: photoconductive liquid crystalline oligothiophene--C60 dyads.

For tailoring solution-processable optoelectronic thin films, a rational strategy with amphiphilic molecular design is proposed. A donor-acceptor dyad consisting of an oligothiophene and C60, when modified with a hydrophilic wedge on one side and a paraffinic wedge on the other (1Amphi), forms over a wide temperature range a photoconducting smectic A liquid crystal having bicontinuous arrays of densely packed donor and acceptor units. In contrast, when modified with only paraffinic wedges (1Lipo), the dyad forms a smectic A liquid crystalline mesophase, which however is poorly conductive.

Amino acid residues interacting with both the bound quinone and coenzyme, pyrroloquinoline quinone, in Escherichia coli membrane-bound glucose dehydrogenase.

The Escherichia coli membrane-bound glucose dehydrogenase (mGDH) as the primary component of the respiratory chain possesses a tightly bound ubiquinone (UQ) flanking pyrroloquinoline quinone (PQQ) as a coenzyme. Several mutants for Asp-354, Asp-466, and Lys-493, located close to PQQ, that were constructed by site-specific mutagenesis were characterized by enzymatic, pulse radiolysis, and EPR analyses. These mutants retained almost no dehydrogenase activity or ability of PQQ reduction.

Superstructure-dependent optical and electrical properties of an unusual face-to-face, pi-stacked, one-dimensional assembly of dehydrobenzo[12]annulene in the crystalline state.

To develop a novel pi-conjugated molecule-based supramolecular assembly, we designed and synthesized trisdehydrotribenzo[12]annulene ([12]DBA) derivative 2 with three carboxyl groups at the periphery. Recrystallization of 2 from DMSO gave a crystal of the solvate 23 DMSO. Crystallographic analysis revealed, to our surprise, that a face-to-face pi-stacked one-dimensional (1D) assembly of 2 was achieved and that the DMSO molecule played a significant role as a "structure-dominant element" in the crystal.

Effect of the heterointerface on transport properties of in situ formed MgO/titanate heterostructured nanowires.

Heterostructured transition metal oxide nanowires are potential candidates to incorporate rich functionalities into nanowire-based devices. Although the oxide heterointerface plays a crucial role in determining the physical properties, the effects of the heterointerface on the oxide nanowire's properties have not been clarified. Here we investigate for the first time the significant role of the heterointerface in determining the transport properties of well-defined MgO/titanate heterostructured nanowires by combining a technique for in situ formation of a oxide heterointerface and microwave conductivity measurement.

Electronegative oligothiophenes fully annelated with hexafluorocyclopentene: synthesis, properties, and intrinsic electron mobility.

Synthesis of hexafluorocyclopenta[c]thiophene-repeated oligothiophenes up to 6-mer has been accomplished. The photophysical and electrochemical properties of these oligomers unambiguously exemplify marked electronegative character without disrupting the effective conjugation. The combination of time-resolved microwave conductivity and transient optical spectroscopy measurements of the 6-mer revealed the intrinsic electron mobility to be as high as 2.

Line edge roughness after development in a positive-tone chemically amplified resist of post-optical lithography investigated by Monte Carlo simulation and a dissolution model.

Line edge roughness (LER) of patterned features in chemically amplified (CA) resists is formed in the acid generation stage and expected to be moderated by the acid diffusion and development process. It is essential to obtain information on the limit of LER in order to realize next-generation lithographies such as electron beam or extreme ultraviolet. Here, we report for the first time a process simulator based on physical and chemical reaction mechanisms.