A simple coarse-grained model for interacting protein complex

ABSTRACT

We present a simple coarse-grained model in which each amino acid residue is represented by one coarse-grained particle for interacting protein complex. In order to determine the coarse-grained potential function of the interaction between amino acid residues, free energy profile as a function of the distance between amino acid side chains is investigated by using all-atom molecular dynamics simulations with thermodynamic integration method. The Langevin dynamics simulation with Gō-like model and our coarse-grained model reproduces homotetramer complex structure of GCN4-pLI and shows that interaction between hydrophobic amino acid residues promote the association of GCN4-pLI monomers.     

Parallel phase-shifting dual-illumination phase unwrapping

We propose a single-shot phase unwrapping technique using a single wavelength and parallel phase-shifting interferometry. In the proposed technique, an object is illuminated by two laser beams, which are emitted from the same laser, and have different illumination angles and polarizations. Two types of object waves generated by the two beams are separately and simultaneously recorded by a polarization-imaging camera. In the path of the reference wave, an array of phase retarders is placed to implement the parallel phase-shifting technique. A highly accurate three-dimensional shape is reconstructed from a single hologram. We numerically simulated the proposed technique and conducted a preliminary experiment to verify its effectiveness. It was confirmed that millimeter-order height, which was several thousand times the wavelength of the laser, can be reconstructed by the proposed technique without wrapping.     

Mechanochromic Photoluminescent Liquid Crystals Containing 5,5′-Bis(2-phenylethynyl)-2,2′-bithiophene

5,5′-Bis(2-phenylethynyl)-2,2′-bithiophene derivative 1 containing dendritic moieties linked through amide groups was synthesized. Compound 1 exhibits a rectangular columnar phase on slow cooling from the isotropic liquid. In contrast, a cubic phase is formed as a metastable liquid-crystalline phase by rapid cooling of the isotropic melt. Mechanical shearing induces a cubic–columnar phase transition, accompanied by the change of a photoluminescent color from yellow-green to green. The infrared spectra of 1 suggest that the mechanical stimuli can induce the partial dissociation of the hydrogen bond. This may lead to more disordering of the π-stacks of chromophores.     

High-speed phase imaging by parallel phase-shifting digital holography

Parallel phase-shifting digital holography can obtain three-dimensional information of a dynamically moving object with high accuracy by using space-division multiplexing of multiple holograms required for phase-shifting interferometry. We demonstrated high-speed parallel phase-shifting digital holography and obtained images of the phase variation of air caused by a compressed gas flow sprayed from a nozzle. In particular, we found the interesting phenomenon of periodic phase distributions. Reconstructed images were obtained at frame rates of 20,000 and 180,000 frames per second.     

Multidimensional angle sensing method using guided-mode resonance

Optical Review - A waveguide grating on a transparent substrate can serve as an optical notch filter owing to guided-mode resonance. The filtering wavelength is highly sensitive to an incidence...     

Si3S-, Si3Se-, Si3Te-Bicyclo[1.1.0]butanes and Si3S2-Bicyclo[1.1.1]pentane

The reaction of trisilirene 1 with propylene sulfide or elemental sulfur produced Si₃S-bicyclo[1.1.0]butane 2, which underwent Si–Si insertion of a second S atom forming Si₃S₂-bicyclo[1.1.1]pentane 3. Analogous reactions of 1 with elemental Se or Te resulted in the formation of heavier analogues of 2, namely, Si₃Se-bicyclo[1.1.0]butane 4 and Si₃Te-bicyclo[1.1.0]butane 5.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.

GRAPHICAL ABSTRACT     

Molecular Flow and Lanthanum -Catalyzed Bond Interchange in Sodium Phosphate Polymers

Abstract

It is observed that sodium phosphate polymers, in which some of the Na⁺ ions have been replaced by La³⁺ ions, are subject to both simple molecular flow and to bond interchange in the glass transition region. These two relaxation mechanisms are separated, and their relative contributions to the shear viscosity are calculated. It is shown that the bond-interchange mechanism is subject to an activation energy of ca. 50 kcal, while that of the molecular flow is of the order of 200 kcal at Tg + 30°C;the latter is of the WLF form. It is further shown that the La³⁺ ions act as cross-links, at least at low concentrations, and that bond interchange occurs at the site of the La³⁺ ions rather than at random along the polymer chain.     

Atom-probe field-ion microscopy of GaAs and GaP

The atom-probe field-ion microscope (atom-probe FIM) was applied for the first time to GaAs and GaP which belong to the III–V compound semiconductors. The general character of the pulsed field-evaporation of GaAs and GaP was quite similar. Ga field-evaporated predominantly in the form of singly charged ions. As and P also field-evaporated mainly as singly charged ions, but their abundances were small compared with Ga⁺. It appears that As (or P) atoms can field-evaporate more easily in the form of AsO⁺ (or PO⁺) in the presence of oxygen on the surface. In all experiments, GaAsⁿ⁺ and GaPⁿ⁺ were rarely detected. After chemical etching the surfaces were covered with oxide films and various oxide ions were detected. The abundance of oxide ions dramatically decreased after field evaporation in hydrogen. No distinct difference between the 〈111〉 orientations of these materials which have zinc-blende structure could be observed. Most of the experimental results obtained were explained in terms of the existing theory of field evaporation. It was concluded that field penetration effects have a considerable influence on the field evaporation processes of these materials as well as on the field ionization processes.     

Parallel two-step phase-shifting digital holography using polarization

We propose an optical implementation of a parallel two-step phase-shifting digital holography that utilizes a polarization technique. The implementation uses a phase-shifting array device consisting of a retarder array attached to an image sensor, and does not require the optical system to image the phase-shifting array device onto the image sensor required for the previously reported optical implementation of the parallel two-step phase-shifting digital holography. Then, the proposed implementation is essentially simple to align and compose. A preliminary experiment showed that the parallel two-step phase-shifting digital holography based on the proposed implementation can remove the conjugate image clinging to the image reconstructed by Fresnel transform alone with DC term suppression. Also, when the reconstruction distance was changed, the qualities of the reconstructed images were quantitatively evaluated by using normalized root-mean-square error. It was clarified that the proposed implementation was superior to other parallel phase-shifting digital holographies and Fresnel transform alone. Thus, the validity of the proposed implementation was confirmed.