A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

Synthesis and characterization of temperature‐ and pH‐sensitive hydrogels based on poly(2‐ethyl‐2‐oxazoline) and poly(D,L‐lactide)

A novel series of temperature‐ and pH‐sensitive hydrogels based on poly(2‐ethyl‐2‐oxazoline) and three‐arm poly(D,L ‐lactide) were synthesized via photocopolymerization. For the creation of polymeric networks, two types of macromers terminated with methacrylate groups were prepared: poly(2‐ethyl‐2‐oxazoline) dimethacrylate and three‐arm poly(D,L ‐lactide) trimethacrylate. The chemical structures were analyzed with ¹H NMR and Fourier transform infrared techniques. The thermal behaviors, morphologies, and swelling properties were measured for the characterization of the polymeric networks. All the poly(2‐ethyl‐2‐oxazoline)/three‐arm poly(D,L ‐lactide)hydrogels provided high water retention capacity and exhibited reversible swelling–shrinking behavior in response to temperature and pH variations. The hydrogels with higher poly(2‐ethyl‐2‐oxazoline) dimethacrylate contents were more effective in raising the swelling ratio and temperature and pH sensitivity. However, higher contents of three‐arm poly(D,L ‐lactide) trimethacrylate produced larger particles and pore sizes in the hydrogels. This study effectively proves that this unique combination of water swellability and biodegradability provides hydrogels with a much wider range of applications in biomedical fields. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1112–1121, 2002     

Enhancedt −3/2 long-time tail for the stress-stress time correlation function

Nonequilibrium molecular dynamics is used to calculate the spectrum of shear viscosity for a Lennard-Jones fluid. The calculated zero-frequency shear viscosity agrees well with experimental argon results for the two state points considered. The low-frequency behavior of shear viscosity is dominated by an ^1/2 cusp. Analysis of the form of this cusp reveals that the stress-stress time correlation function exhibits at ^–3/2 long-time tail. It is shown that for the state points studied, the amplitude of this long-time tail is between 12 and 150 times larger than what has been predicted theoretically. If the low-frequency results are truly asymptotic, they imply that the cross and potential contributions to the Kubo-Green integrand for shear viscosity exhibit at ^–3/2 long-time tail. This result contradicts the established theory of such processes.     

Simulations of the active transport of a neutral solute based on a kinase-channel-phosphatase topology

Simulations of coupled interactions involving two opposite enzymatic reactions, solute diffusions, and electrostatic interactions between membrane charges and charged solutes were conducted under a fixed kinase-channel-phosphatase (KCP) topology oriented from the outside to the inside of a porous membrane structure. Depending on the kinase and phosphatase locations, we recently demonstrated that an active transport of a phosphorylated substrate may occur via the opposite topology, that is, a PCK topology. The present analysis demonstrates that, under a KCP membrane topology, which also behaves as a specific ATP-dependent transporter, the active transport of a neutral substrate may occur. This analogous active transport appears to be dependent on the phosphatase location and on the membrane surface potentials. A broad analysis of the role played by the main parameters taken into account in the model was conducted in order to define precisely the physico-chemical conditions and the membrane topology needed for the highest active transports within the shortest time.     

冲击压缩下玻璃等脆性材料中失效波的研究进展

失效波的研究始于Rasorenov和Kanel发现K1 9玻璃样品后自由表面速度时程曲线上有反常再压缩信号。失效波是二十世纪九十年代冲击动力学研究领域的一个重要发现 ,它是指在一维平面应变冲击压缩下 ,在玻璃等脆性材料中由冲击波引起的一种独特的失效或破坏现象。较为系统地回顾近年来对失效波的研究工作 ,评述了研究现状、最新结果、发展趋势、研究方法和实验手段 ,对尚存的问题进行了分析讨论 ,并介绍了玻璃材料的基本特性。最后简单汇报了作者在这方面的研究工作和取得的阶段性结果。     

Size-dependent electron chemical potential: Effect on particle charging

Electrostatic charging of particles of identical composition, but different sizes, is a poorly understood phenomenon that may be of importance in dust storms, generation of lightning, numerous technological applications involving solid particulates, and in the agglomeration of lunar dust and inter-stellar dust clouds. We show that under optical excitation, the relative magnitude of surface to volume de-excitation gives size-dependent electron and hole concentrations. The consequent differences in chemical potentials can lead to charge transfer between particles of different size. The direction of charge transfer, from large to small or vice versa, depends critically on the properties of the materials.     

A dissipation‐free numerical method to solve one‐dimensional hyperbolic flow equations

In this paper, a numerical method to capture the shock wave propagation in 1‐dimensional fluid flow problems with 0 numerical dissipation is presented. Instead of using a traditional discrete grid, the new numerical method is built on a range‐discrete grid, which is obtained by a direct subdivision of values around the shock area. The range discrete grid consists of 2 types: continuous points and shock points. Numerical solution is achieved by tracking characteristics and shocks for the movements of continuous and shock points, respectively. Shocks can be generated or eliminated when triggering entropy conditions in a marking step. The method is conservative and total variation diminishing. We apply this new method to several examples, including solving Burgers equation for aerodynamics, Buckley‐Leverett equation for fractional flow in porous media, and the classical traffic flow. The solutions were verified against analytical solutions under simple conditions. Comparisons with several other traditional methods showed that the new method achieves a higher accuracy in capturing the shock while using much less grid number. The new method can serve as a fast tool to assess the shock wave propagation in various flow problems with good accuracy.     

Shock waves for the hyperbolic balance laws with discontinuous sources

In this paper, we are concerned with the behavior of shock waves in a 2 × 2 balance law with discontinuous source terms. We obtain the existence of a local shock wave solution of this problem and deduce that the discontinuous source terms create a weak discontinuity in this solution. Copyright © 2013 John Wiley & Sons, Ltd.     

The research on temperature measurement based on polarization dependent loss

This paper analyzes the properties of reflected polarization dependent loss of apodized fiber Bragg gratings with temperature effective. We simulates reflected spectrum and polarization dependent loss of the apodized fiber Bragg gratings. The reflected spectrum and polarization dependent loss are measured under different temperatures. The analysis results show that reflected polarization dependent loss presents two peaks which shift an equal proportion to long wavelength with temperature increasing and have very good stability so we propose an idea that use polarization dependent loss as temperature sensor measurement parameters. The results show that the accuracy of measurement can be increased almost by one order of magnitude.