Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc.     

Experimental demonstration of the induction synchrotron

We report an experimental demonstration of the induction synchrotron, the concept of which has been proposed as a future accelerator for the second generation of neutrino factory or hadron collider. The induction synchrotron supports a superbunch and a superbunch permits more charge to be accelerated while observing the constraints of the transverse space-charge limit. By using a newly developed induction acceleration system instead of radio-wave acceleration devices, a single proton bunch injected from the 500 MeV booster ring and captured by the barrier bucket created by the induction step voltages was accelerated to 6 GeV in the KEK proton synchrotron.     

Photo-alignment Property of Azobenzene-containing Polyimide Films Swollen by Alkyl-amine

Photo-alignment efficiency of polyimide containing azobenzene in the backbone structure (Azo-PI) is significantly enhanced by exposing the precursor (polyamic acid: Azo-PAA) film to alkyl-amine vapor prior to photo-alignment. In this study, we have investigated the relationships between the alkyl-amine vapor treatment time, the swelling ratio of Azo-PAA films, and the photo-induced in-plane anisotropy. We found that: the Azo-PAA film swells on exposure to alkyl-amine vapor, and the swelling finally saturates; and the photo-induced in-plane anisotropy is correlated very closely with the swelling ratio. In addition, we pointed out the importance of the process order of alkyl-amine vapor treatment and photo-alignment.     

Application of nanoscale packed capillary liquid chromatography (75 μm id) and capillary zone electrophoresis/electrospray ionization mass spectrometry to the analysis of macrolide antibiotics

Nanoscale separation techniques, nanoscale packed capillary columns (75 μm id), and capillary zone electrophoresis (CZE), on-line with electrospray mass spectrometry (ESI/MS), were applied to the separation of a series of ten macrolide antibiotics. Both techniques use sub-microliter-per-minute flow rates through the analytical column and therefore require an electrospray probe that incorporates coaxial sheath flow. Positive ion electrospray mass spectra of these compounds yielded mainly protonated molecules. Fragmentation to yield structurally significant fragment ions was achieved by collision-induced dissociation (CID) at increased skimmer voltages. Separations were achieved using both techniques, with CZE/ESI/MS showing improved peak shapes and detection limits combined with faster analysis times. Nanoscale packed capillary columns provided better chromatographic resolution and was less susceptible to peak broadening caused by overloading of the analytes.     

Molecular-level chiral discrimination and induction

The review describes the mechanism of chiral discrimination of racemic amines upon crystallization and the induction of chirality in organic reactions by using them as chiral auxiliaries. In order to form conglomerates, which can be resolved into the two enantiomers upon alternative seeding, both formation and packing of 2₁-columns are essentially very important. On the other hand, in order to achieve high efficiency in resolution through diastereomeric salt formation, which is the most practical method, one of a pair of diastereomeric salts derived from a racemic amine and an enantiomerically pure resolving agent should at least have two 2₁-columns and planar boundary surfaces in its crystal structure. On the basis of this knowledge, we developed several artificial chiral auxiliaries such as erythro-2-amino-1,2-diphenylethanol,cis-2-amino-1-acenaphthenol, andcis-2-amino-3,3-dimethyl-1-indanol. These were found to be very efficient chiral auxiliaries in asymmetric inductions: alkylation of chiral imines, catalytic borane-reduction, and alkylation of chiral N-acylated oxazolidinone.     

Study of Ag/Si(111) submonolayer interface: I. Electronic structure by angle-resolved UPS

Angle-resolved ultraviolet photoelectron spectra have been measured for well defined Ag/Si(111) submonolayer interfaces of (1) $\text{Si(111)(}\text{3}\text{×}\text{3}\text{)R30°-Ag}$, (2) “Si(111)(6 × 1)-Ag”, and (3) Ag/Si(111) as deposited at room temperature. Non-dispersive and very narrow (FWHM ～ 0.4–0.5 eV) Ag 4d derived peaks are found at 5.6 and 6.5 eV below the Fermi level for surface (1) and at 5.3 and 6.0 eV for surface (2). Dispersions of sp “binding” states in the energy range between E_F and Ag 4d states have been precisely determined for surface (1). Electronic structures similar to those of the Ag(111) surface, including the surface state near E_F, have been observed for surface (3).     

Adsorption of thiolates to singly coordinated sites on Au111 evidenced by photoelectron diffraction

The adsorption structure of methylthiolate (CH3S) adsorbed on Au(111), a long-standing controversial issue, has been unambiguously determined by scanned-energy and scanned-angle S 2p photoelectron diffraction. The methylthiolate molecules are found to occupy atop sites with a S-Au distance of 2.42 +/- 0.03 A. The angular distribution of the S 2p photoelectrons due to forward scattering reveals that the S-C bond is inclined by approximately 50 degrees from the surface normal towards both the [211] and [121] (nearest-neighbor thiolate) directions.     

Characterization of the mod 3 cohomology of

It is shown that the mod 3 cohomology of a homotopy associative mod 3 -space which is rationally equivalent to the Lie group and which has integral 3-torsion is isomorphic to that of as a Hopf algebra over the mod 3 Steenrod algebra.

     

Spiral structures in magnetized rotating plasmas

A theory of spiral structure formation has been formulated to show that spiral structures are rather basic entities in magnetized rotating plasmas subjected to various types of instabilities such as collisional drift wave instability, flute mode instability due to centrifugal force, and Kelvin-Helmhotz instability. The characteristic features of spiral structures observed experimentally in electron cyclotron resonance plasmas are reproduced by our theory.     

Quantitative analysis of organic additive content in a polymer by ToF-SIMS with PCA

Quantitative analysis of organic materials by ToF-SIMS is intrinsically difficult because of their tendency to decompose under ion irradiation. In this study, we applied principal component analysis (PCA) as a means of compensation for the spectral degradation caused by this decomposition and thus improve the accuracy of the quantitative analysis, using as models two organic additives of quite different composition and vulnerability to decomposition under ion irradiation, in polystyrene. This enables the extraction of a principal component related to their content that is independent of the decomposition. The effectiveness of this approach in quantitative analysis of organic additives content in polymers without loss in accuracy due to spectral degradation will be discussed.