Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Temperature Characteristics of Vibrating Type Sensor Using Micromachined Optical Fiber-Tip

An optical sensor using a quartz core microcantilever was fabricated by etching clad layer from optical fiber. The temperature dependence of the resonance frequency of this sensor was measured in atmosphere and water. The temperature coefficient of the resonance frequency in water was 1.3×10⁻³/°C, which was about one order larger than that (2.3×10⁻⁴/°C) in atmosphere. This was caused by increase of additional mass due to temperature dependence of the viscosity of water, while, the increase of the resonance frequency in atmosphere was caused by temperature dependence of Young’s modulus of the quartz core. These results were evaluated theoretically using a “string-of-beads” model.     

Evaluation of elastic, elastic-plastic properties of thin Pt wire by?mechanical bending test

A testing methodology to determine the elastic-plastic properties of thin metallic wires is reported. A small-scaled bending test of Pt thin wire and the corresponding finite element analysis are performed. By fitting the load-displacement relationship obtained by finite element analysis to the experimental one, the elastic, elastic-plastic properties of Pt wire are successfully determined.     

Thermoelastic damping of the axisymmetric vibration of circular plate resonators

Thermoelastic damping is recognized as a significant loss mechanism at room temperature in micro-scale circular plate resonators. In this paper, the governing equations of coupled thermoelastic problems are established for axisymmetric out-of-plane vibration of circular plate. Then the analytical expression for thermoelastic damping is obtained. The effects of environmental temperature, plate dimensions and boundary conditions on the thermoelastic damping are studied.     

Charge-order pattern of the low-temperature phase from a monoclinic single domain of NaV2O5 uniquely determined by resonant x-ray scattering

The present resonant x-ray scattering has been performed on a monoclinically split single domain of NaV(2)O(5). The observation of a critically enhanced contrast between V(4+) and V(5+) ions has led us to the unequivocal conclusion of the charge-order pattern of the low-temperature phase of NaV(2)O(5) below T(c) = 35 K. In spite of the possible four types of configuration of the zigzag-type charge-order patterns in the ab plane (A,A',B and B'), the stacking sequence along the c axis is determined as the AAA'A' type by comparison with model calculations.     

Photoelectrochemical decomposition of water on nanocrystalline BiVO4 film electrodes under visible light

The nanocrystalline BiVO4 film electrode on conducting glass showed an excellent efficiency (IPCE = 29% at 420 nm) for the decomposition of water under visible light.