Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover

We propose a conformational search method to find a global minimum energy structure for protein systems. The simulated annealing is a powerful method for local conformational search. On the other hand, the genetic crossover can search the global conformational space. Our method incorporates these attractive features of the simulated annealing and genetic crossover. In the previous works, we have been using the Monte Carlo algorithm for simulated annealing. In the present work, we use the molecular dynamics algorithm instead. To examine the effectiveness of our method, we compared our results with those of the normal simulated annealing molecular dynamics simulations by using an α-helical miniprotein. We used genetic two-point crossover here. The conformations, which have lower energy than those obtained from the conventional simulated annealing, were obtained.     

Differential Effects of Cold Exposure on Gene Expression Profiles in White Versus Brown Adipose Tissue

The thermogenic function of brown adipose tissue (BAT) is known to be markedly elevated when animals are exposed to the cold, and intensive studies have been carried out to understand the molecular basis enabling effective thermogenesis in cold-exposed animals. In this study, we used microarray analysis to examine the effects of cold exposure of animals on their gene expression profiles in white adipose tissue (WAT), which seems to function as a counterpart tissue of BAT. The results indicate that the effects of cold exposure on the gene expression profiles of WAT were much more moderate than the effects on those of BAT. Possible reasons for the different responses of BAT and WAT to cold exposure are discussed.     

Liquid phase formation of alkyl- and perfluoro-phosphonic acid derived monolayers on magnesium alloy AZ31 and their chemical properties

Alkyl- and perfluoro-phosphonic acid derived SAMs were successfully formed on Mg alloy by liquid phase method for the first time. The chemical and anticorrosive properties of the prepared SAMs on magnesium alloys were characterized using contact angle measurements, X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and electrochemical measurements. Water contact angle measurements revealed that the maximum advancing/receding water contact angles of n-octyl (OP: CH(3)(CH(2))(7)PO(OH)(2)), n-dodecyl (DP: CH(3)(CH(2))(11)PO(OH)(2)), n-octadecyl (ODP: CH(3)(CH(2))(17)PO(OH)(2)) phosphonic acid, and 2-(perfluorohexyl)ethyl (PFEP: CF(3)(CF(2))(5)CH(2)CH(2)PO(OH)(2)) phosphonic acid were 105.1/64.7°, 108.3/69.6°, 111.9/75.2°, and 115.2/67.4° respectively. In the case of alkylphosphonic acid SAMs (OP, DP, and ODP), the advancing and receding water contact angles increased with an increase in the preparation time. The angle-resolved XPS (AR-XPS) data revealed that the film thicknesses of the OP, DP, ODP, PFEP on Mg alloy were estimated to be 0.8, 1.2, 1.7, and 1.1 nm, respectively. The XPS O 1s data support that the phosphonic acid derived SAM is covalently bound to the oxide or hydroxide surface of the Mg alloy in a monodenate or bidenate manner. Chemical stability of the alkyl- and perfluoro-phosphonic acid modified Mg alloy surfaces was investigated using aqueous solutions at pH=4.0, 7.0, and 10.0. The contact angles of OP, DP, and PFEP modified Mg surface decreased rapidly within the first 5 min after immersion in all the aqueous solutions and were less than 20°. On the other hand, the contact angles of the ODP modified Mg alloy after immersion in aqueous solutions at pH 4, 7 and 10 for 5 min were 45.1°, 89.3,° and 85.5°, respectively. The ODP modified Mg alloy had highest chemical stability in four types of the phosphonic acid derived SAMs used in this study, indicating that the molecular density of ODP on Mg alloy would be higher than those of OP, DP, PFEP on Mg alloy. The corrosion resistance of ODP modified Mg alloy was investigated by potentiodynamic polarization curve measurements. The ODP modified Mg alloy exhibits protective properties in a solution containing Cl(-) ions compared to unmodified Mg alloy.     

Transformation of ionic liquid into carbon nanotubes in confined nanospace

We have developed a two-step filling process for the nano-reaction of ionic liquid in a tip-closed SWNT, where fullerenes are inserted at the end of the host SWNT as a plug to prevent the leakage of the confined ionic liquid during heat treatment.     

A coumarin-based fluorescent probe for Hg2+ and Ag+ with an N'-acetylthioureido group as a fluorescence switch

For detection of Hg(2+) and Ag(+), we have developed a coumarin-based probe with an N'-acetylthioureido group as a novel fluorescence switch, in which the hydrogen bond formation between the N-hydrogen and the acetyl O atom markedly increases the susceptibility of the probe toward desulfurization by Hg(2+) and Ag(+).     

Multiple Coulomb excitation of a 70Ge beam and the interpretation of the 02 + state as a deformed intruder

Electromagnetic properties of the low-lying states in a ⁷⁰Ge nucleus were studied through the multiple Coulomb excitation of a ⁷⁰Ge beam with a ^natPb target. Relative γ-ray intensities were measured as a function of emission angle relative to the scattered projectile. Sixteen E2 matrix elements, including diagonal ones, for 6 low-lying states have been determined using the least-squares search code GOSIA. The expectation values 〈Q ²〉 of 0₁ ⁺ and 0₂ ⁺ states in ⁷⁰Ge are compared with those in ^{72, 74, 76}Ge. Simple mixing calculations indicate that the 0₂ ⁺ states in ⁷⁰Ge and ⁷²Se can be treated as deformed intruder states. It is shown that the deformed intruder becomes the ground state in ⁷⁴Kr. These interpretations of the 0₂ ⁺ states in this region are compared with the potential-energy surface calculations by the Nilsson-Strutinsky model, which allow to interpret the experimental results in a qualitative way from the theoretical point of view. Received: 2 September 2002 / Accepted: 5 November 2002 / Published online: 25 February 2003 RID="a" ID="a"e-mail: sugawara@pf.it-chiba.ac.jp Communicated by D. Schwalm