Formation process of cyclodextrin necklace-analysis of hydrogen bonding on a molecular level

By means of scanning tunneling microscopy (STM), we succeeded for the first time in the quantitative analysis of the intramolecular conformation of a supramolecule, cyclodextrin (CyD) necklace, driven by hydrogen bonding. Contrary to the current model, based on macroscopic analyses, which indicates that all CyDs are arranged in head-to-head or tail-to-tail (secondary-secondary or primary-primary hydrogen bonding) conformation, about 20% head-to-tail (primary-secondary hydrogen bonding) conformation was found to exist in the molecule. In addition, comparing the STM results with the theoretical model of the necklace formation, the formation ratio of the tail-to-tail and head-to-tail conformations due to the strength difference between primary-primary and primary-secondary hydrogen bonds of CyDs was directly obtained, for the first time, to be 2:1.     

Conformational Changes of the Troponin—Tropomyosin Complex on F-Actin Observed by Fluorescence Resonance Energy Transfer Measurements

Contraction of vertebrate striated muscle is regulated by the strong Ca²⁺-dependent interaction among troponin (Tn), tropomyosin (Tm), and actin on the thin filament. Using fluorescence resonance energy transfer (FRET), the interactions between Tm and the Tn complex or between Tm and the Tn subunit, TnI or TnC, with or without other troponin subunits, were characterized in the presence or absence of F-actin and Ca²⁺ ions. Cys-190 of Tm was selectively labeled with the acceptor probe, 4-dimethylaminophenylazophenyl 4-maleimide. Troponin was selectively labeled at position 9 or 133 of TnI and position 98 of TnC with a donor probe, 5-(2-iodoacetylaminoethyl)aminonaphtha lene 1-sulfonic acid. FRET measurements indicate that the interaction between TnI and Tm alone is very weak, but that in the presence of F-actin, TnI binds to the proper binding site on Tm even in the absence of TnT. The distances between Cys-190 of Tm on F-actin and Cys-9 or Cys-133 of Tnl or Cys-98 of TnC in the reconstituted Tn were determined to be 52.8, 53.7, Å and 56.5 Å, respectively, in the absence of Ca²⁺, indicating that the Tnl—TnC complex, the globular portion of Tn, is located near Cys-190 of Tm on the reconstituted thin filaments. Upon binding of Ca²⁺ to TnC, these distances increased by 5.6 and 1.4 Å or decreased by 5.4 Å, respectively. These Ca²⁺-induced changes in Tn—Tm seem to occur only when F-actin is present, suggesting that the stable complex formation of TnI with the outer domain of F-actin upon removal of Ca²⁺ is a very important event during inhibition.     

Primal-dual path following method for nonlinear semi-infinite programs with semi-definite constraints

Mathematical Programming - In this paper, we propose a primal-dual path following method for nonlinear semi-infinite semi-definite programs with infinitely many convex inequality constraints,...     

Observation of giant resonance phenomena in the two-step mechanism of electron-Xe collision

We report an (e,2e) binding energy spectrum of Xe obtained at an impact energy of 2.1 keV, which covers the binding energy range up to 220 eV. The result is directly compared with data from high-energy photoelectron spectroscopy. It is found that an (e,2e)-specific, very broad band appears at around 120 eV, although in other energy regions the binding energy spectra by the two methods are in good agreement. The presence of such a band is revealed for the first time, which can be attributed to the second-order effects of the electron-target interaction that involves giant resonance phenomena of the Xe 4d electron.     

Simulation of DNA motion in a microchannel using stochastic rotation dynamics

The authors propose a method to simulate the DNA motion in microchannels of complex geometry. It is based on stochastic rotation dynamics using a new scheme for the boundary condition. The method enables them to define a boundary wall of arbitrary shape and to describe a wall moving at an arbitrary velocity. As an application, they simulate the motion of DNA in Poiseuille flow between two parallel planes and show that DNA molecules tend to concentrate near the center of the channel in agreement with experimental results.     

Scenarios of heterogeneous nucleation and growth studied by cell dynamics simulation

The dynamics of phase transformation due to homogeneous nucleation has long been analyzed using the classic Kolmogorov-Johnson-Mehl-Avrami (KJMA) theory. However, the dynamics of phase transformation due to heterogeneous nucleation has not been studied systematically even though it is vitally important technologically. In this report, the author studies the dynamics of heterogeneous nucleation theoretically and systematically using the phenomenological time-dependent Ginzburg-Landau (TDGL)-type model combined with the cell dynamics method. In this study the author focuses on the dynamics of phase transformation when the material is sandwiched by two supporting substrates. This model is supposed to simulate phase change storage media. Since both homogeneous and heterogeneous nucleations can occur simultaneously, the author predicts a few scenarios of phase transformation including homogeneous nucleation regime, heterogeneous nucleation regime, and the homogeneous-heterogeneous coexistence regime. These predictions are directly confirmed by numerical simulation using the TDGL model. The outcome of the study was that the KJMA formula has limited use when heterogeneous nucleation exists, but it could still give some information about the microscopic mechanism of phase transformation at various stages during phase transformation.     

Dynamics of condensation of wetting layer in time-dependent Ginzburg-Landau model

The dynamics of liquid condensation on a substrate or within a capillary is studied when the wetting film grows via interface-limited growth. We use a phenomenological time-dependent Ginzburg-Landau (TDGL)-type model with long-range substrate potential. Using an order parameter, which does not directly represent the density, we can derive an analytic formula for the interfacial growth velocity that is directly related to the substrate potential. Using this analytic expression the growth of wetting film is shown to conform to a power-law-type growth, which is due to the presence of a long-range dispersion force.     

First total synthesis of antitumor natural product (+)- and (-)-pericosine A: determination of absolute stereo structure

The first total synthesis of (+)- and (-)-pericosine A has been achieved, enabling the revision and determination of the absolute configuration of this antitumor natural product as methyl (3S,4S,5S,6S)-6-chloro-3,4,5-trihydroxy-1-cyclohexene-1-carboxylate. Every step of this total synthesis proceeded well with excellent stereoselectivity. Structures of the intermediates in crucial steps were confirmed by detailed 2D NMR analysis.