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Molecular and quantum mechanical studies on the monomer recognition of a highly-regular β-helical antifreeze protein

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Science China Chemistry 2004年第1期47卷 34-40页

作者： YANG Zuoyin, JIA Zongchao, LIU Ruozhuang & CHEN GuangjuDepartment of Chemistry, Beijing Normal University, Beijing 100875, China Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, China Department of Biochemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada Department of Chemistry Beijing Normal University Beijing China Faculty of Science Beijing University of Chemical Technology Beijing China Department of Biochemistry Queenś University Kingston Canada

The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomer? β-sheets would be involved in interaction area and the side chains on two p-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the twoβ-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two TCTs mainly depends on inter-molecular hydroxyls. Therefore, our results demonstrate that during the course of interaction the most favorable association of TmAFPs is via their β-sheets.

关键词： antifreeze protein, recognition, dynamics simulation, molecular mechanics, quantum chemistry.

Supersymmetry and Shape Invariance of Hartmann Potential and Ring-Shaped Oscillator Potential in the γ and θ Dimensions of Spherical Polar Coordinates

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Communications in Theoretical Physics 2002年第8期38卷 139-142页

作者： QIAN Shang-Wu HUANG Bo-Wen WANG De-Yun GU Zhi-Yu Physics Department Peking University Beijing 100871 China Physics Department Capital Normal University Beijing 100037 China Physics Department Capital Normal University Beijing 100037 China Physics Department Capital Normal University Beijing 100037 China

This article shows that in spherical polar coordinates, some noncentral separable potentials have super-symmetry and shape invariance in the r and θ dimensions, we choose Hartmann potential and ring-shaped oscillator astwo important examples, thus in principle the energy eigenvalues and energy eigenfunctions of such the potentials in ther and θ dimensions can be obtained by the method of supersymmetric quantum mechanics. Here we use an alternativemethod to get the required results.

关键词： Hartmann potential, ring-shaped oscillator potential, supersymmetric quantum mechanics, shapeinvariance, noncentral separable potential, spherical polar coordinates

Monte Carlo Hamiltonian: Linear Potentials

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Communications in Theoretical Physics 2002年第5期38卷 561-565页

作者： LUO Xiang-Qian LIU Jin-Jiang HUANG Chun-Qing JIANG Jun-Qin Helmut KROGER Department of Physics Zhongshan University Guangzhou 510275 China Department of Physics Zhongshan University Guangzhou 510275 China Department of Physics Zhongshan University Guangzhou 510275 China Department of Physics Zhongshan University Guangzhou 510275 China 2Département de Physique Université Laval Québec Québec G1K 7P4 Canada

We further study the validity of the Monte Carlo Hamiltonian method. The advantage of the method,in comparison with the standard Monte Carlo Lagrangian approach, is its capability to study the excited states. Weconsider two quantum mechanical models: a symmetric one V(x) = |x|/2; and an asymmetric one V(x) = ∞, forx ＜ 0 and V(x) = x, for x ≥ 0. The results for the spectrum, wave functions and thermodynamical observables are inagreement with the analytical or Runge-Kutta calculations.

关键词： Monte Carlo method, quantum mechanics, computational physics

Structure of cis-[Pt(NH_(3))(2-picoline)]^(2+)and DNA adduct and its bonding characteristics

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Science China Chemistry 2004年第1期47卷 67-74页

作者： JIA Muxin, LIU Kai, YANG Zuoyin & CHEN GuangjuDepartment of Chemistry, Beijing Normal University, Beijing 100875, China Beijing General Research Institute of Mining and Metullargy, Beijing 100044, China Department of Chemistry Beijing Normal University Beijing China Beijing General Research Institute of Mining and Metullargy Beijing China

Several methods including molecular mechanics, molecular dynamics, ONIOM that combines quantum chemistry with molecular mechanics and standard quantum chemistry are used to study the configuration and electron structures of an adduct of the DNA segment d(ATACATG*G*TACATA)·d(TATGTACCATGTAT) with cis-[Pt(NH3)(2-Picoline)]2+. The investigation shows that the configuration optimized by ONIOM is similar to that determined by NMR. Strong chemical bonds between Pt of the complex and two N7s of neighboring guanines in the DNA duplex and hydrogen bond between the NH3 of the complex and O6 of a nearby guanine have a large impact on the configuration of the adduct. Chemical bonds, the aforementioned hydrogen bond, and the interaction between a methyl of the complex and a methyl of the base in close proximity are critical for the complex to specifically recognize DNA.

关键词： cis-[PtCl2(NH3)(2-Pic)], DNA segment, ONIOM, molecular mechanics, molecular dynamics.

Molecular simulation of alkyl monolayers on the Si(111)surface

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Science China Chemistry 2003年第2期46卷 168-175页

作者：苑世领蔡政亭肖莉徐桂英刘永军 Institute of Theoretical Chemistry Shandong University Institute of Colloid and Interface Chemistry Shandong University Jinan 250100 China Institute of Colloid and Interface Chemistry Shandong University

The structure of twelve-carbon monolayers on the H-terminated Si(111) surface is inves-tigated by molecular simulation method. The best substitution percent on Si(111) surface obtained via molecular mechanics calculation is equal to 50%, and the (88) simulated cell can be used to depict the structure of alkyl monolayer on Si surface. After two-dimensional cell containing alkyl chains and four-layer Si(111) crystal at the substitution 50% is constructed, the densely packed and well-ordered monolayer on Si(111) surface can be shown through energy minimization in the suitable-size simulation cell. These simulation results are in good agreement with the experiments. These conclusions show that molecular simulation can provide otherwise inaccessible mesoscopic information at the molecular level, and can be considered as an adjunct to experiments.

关键词： monolayer film, Si(111) surface, molecular simulation, molecular mechanics, alkyl chain.

RECENT PROGRESS IN THE PROJECT OF SPACE SOLAR TELESCOPE

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空间科学学报 2002年第Z1期22卷 21-28页

作者： JIN Shengzhen WANG Sen YANG Shimo JIANG Aimin SUN Caihong National Astronomical Observatory The Chinese Academy of Sciences Beijing 100012 P. R. China National Astronomical Observatory The Chinese Academy of Sciences Beijing 100012 P. R. China National Astronomical Observatory The Chinese Academy of Sciences Beijing 100012 P. R. China National Astronomical Observatory The Chinese Academy of Sciences Beijing 100012 P. R. China National Astronomical Observatory The Chinese Academy of Sciences Beijing 100012 P. R. China

In this paper, we introduce some process of the project of Space Solar Telescope in recent two years. The astronomic requirements have been further identified,the mission and operation requirements have been assessed, and some critical technologies have been performed. According to the time schedule, it is esti mated that the engineering model of the spacecraft would be completed and put into test operation in the end of 2004 and the spacecraft would be launched in about 2007.

关键词： Main telescope, mechanics, Electronics

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脆性单颗粒之动态损伤和破碎

岩石力学与工程学报 2003年第Z1期22卷 2138-2144页

作者：周锦添武生智黄凯珠

Breakage, comminution, crushing and fragmentation of brittle solids under dynamic impacts are an important applied mechanics and rock mechanics problem. In civil engineering applications, impact-induced-fragmentation relates to crushing of rock mass during mining process, tunneling, and aggregate production. The main objective of this paper is to outline some of our recent experimental, analytical and numerical efforts in studying the dynamic fragmentation process in brittle particle. First, an analytical solution of a solid sphere compressed dynamically between two rigid flat platens is derived analytically. Secondly, a sequence of double impact tests on spheres were conducted using an impactor Dynatup 8250 at HKUST, with both impact velocity and contact force at the impactor measured accurately. Finally, a newly developed computer program, DIFAR, is used to investigate the mechanism of dynamic fragmentation. The paper will summarize and discuss briefly all three aspects of our comprehensive approach.

关键词： damage mechanics, fragmentation, dynamic impact, brittle particles