关键词： Brownian motion   fluctuations   friction   heat transfer   molecular dynamics method   nonequilibrium thermodynamics   probability   statistical mechanics   stochastic processes  

摘要： The general form for the probability density and for the transition probability of a nonequilibrium system is given. Maximization of the latter gives a generalized fluctuation-dissipation theorem by providing a molecular basis for Langevin's friction force that avoids continuum hydrodynamics. The result shows that the friction coefficient must be proportional to the variance of the stochastic equations of motion. Setting the variance to zero but keeping the friction coefficient nonzero reduces the theory to a Hoover thermostat without explicit constraint, although such a limit violates the physical requirement of proportionality between the dissipation and the fluctuation. A stochastic molecular dynamics algorithm is developed for both equilibrium and nonequilibrium systems, which is tested for steady heat flow and for a time-varying, driven Brownian particle.

关键词： .rate-limiting   Hairpins   Mechanical Folding   Kinetics of RNA   RNA folding   new kinetic   folding of RNA   low force   base stack  

摘要： Based on an ensemble of kinetically accessible conformations, we propose anew analytical model for RNA folding kinetics. The model gives populational kinetics, kinetic rates, transition states, and pathways from the rate matrix. Applications of the new kinetic model to mechanical folding of RNA hairpins such as trans-activation-responsive RNA reveal distinct kinetic behaviors in different force regimes, from zero force to forces much stronger than the critical force for the folding-unfolding transition. In the absence of force or a low force, folding can be initiated (nucleated) at any position by forming the first base stack and there exist many pathways for the folding process. In contrast, for a higher force, the folding/unfolding would predominantly proceed along a single zipping/unzipping pathway. Studies for different hairpin-forming sequences indicate that depending on the nucleotide sequence, a kinetic intermediate can emerge in the low force regime but disappear in high force regime, and a new kinetic intermediate, which is absent in the low and high force regimes, can emerge in the medium force range. Variations of the force lead to changes in folding cooperativity and rate-limiting steps. The predicted network of pathways for trans-activation-responsive RNA suggests two parallel dominant pathways. The rate-limiting folding steps (at f = 8 pN) are the formation of specific basepairs that are 2-4 basepairs away from the loop. At a higher force (f = 11 pN), the folding rate is controlled by the formation of the bulge loop. The predicted rates and transition states are in good agreement with the experimental data for a broad force regime.

关键词： Molecular dynamics (MD)   Polymer-bonded explosive (PBX)   Binding energies   Mechanical property   Detonation performance  

摘要： To investigate the effect of polymer binders on the moncrexplosive, molecular dynamics simulations were performed to study the binding energies, mechanical properties, and detonation performances or the bicyclo-HMX-based polymer-bonded explosives (PBXs). The results show that the binding energies on different crystalline surfaces of bicyclo-HMX decrease in the order of (0 1 0) > (1 0 0) > (0 0 1). On each crystalline surface, binding properties of different polymers with the same chain segment are different from each other, while those of the polymers in the same content decrease in the sequence of PVDF > F-2311 > F-2314 approximate to PCTFE. The mechanical properties of a dozen of model systems (elastic coefficients, various moduli, Cauchy pressure, and Poisson's ratio) have been obtained. It is found that mechanical properties are effectively improved by adding small amounts of fluorine polymers, and the overall effect of fluorine polymers on three crystalline surfaces of bicyclo-HMX changes in the order of (0 1 0) > (0 0 1) approximate to (1 0 0). In comparison with the base explosive, detonation performances of the PBXs decrease slightly, but they are still superior to TNT. These suggestions may be useful for the formulation design of bicyclo-HMX-based PBXs. Crown Copyright (C) 2008 Published by Elsevier B.V. All rights reserved.

关键词： LETTERS to the editor   MOLECULAR dynamics  

摘要： We use ab initio steered molecular dynamics to investigate the mechanically induced ring opening of cyclobutene. We show that the dynamical results can be considered in terms of a force-modified potential, energy surface (FMPES). We show how the minimal energy paths for the two possible competing conrotatory and disrotatory ring-opening reactions are affected by external force. We also locate minimal energy pathways in the presence of applied external force and show that the reactant, product, and transition state geometries are altered by the application of external force. The largest effects are on the transition state geometries and barrier heights. Our results provide a framework for future investigations of the role of external force on chemical reactivity.

关键词： URANIUM   RESEARCH   SOLUTION (Chemistry)   QUANTUM theory   MOLECULAR dynamics   HARTREE-Fock approximation   ANGULAR distribution (Nuclear physics)   X-ray scattering  

摘要： The structure and dynamics of the stable four-times positively charged uranium(IV) cation in aqueous solution have been investigated by ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation at the Hartree-Fock double-zeta quantum mechanical level. The QMCF-MD approach enables investigations with the accuracy of a quantum mechanics/molecular mechanics approach without the need for the construction of solute-solvent potentials. Angular distribution functions;radial distribution functions;coordination numbers of the first, second, and third shell (9, 19, and 44, respectively);coordination number distribution functions;tilt- and Theta-angle distribution functions;as well as local density corrected triangle distribution functions have been employed for the evaluation of the hydrated ion's structure. Special attention was paid to the determination of the geometry of the first hydration layer, and the results were compared to experimental large-angle X-ray scattering and extended X-ray absorption fine structure data. The solvent dynamics around the ion were also investigated using mean ligand residence times and related data and, resulting from the unavailability of any experimental data, were compared to ions with similar properties.

关键词： 国际论坛   机械制造   持续发展   技术   创新   随访   机床行业   经济形势  

摘要： 热热闹闹的CIMT2009展会于2009年4月11日顺利落下帷幕,在目前不够乐观的经济形势下,此次展会的良好效果成为2009年机床行业奋起抬头的一个好兆头。展会期间,我刊也派出各路记者精英,对部分参展商进行了更深入的采访,以期为行业的信息沟通及企业的进一步发展起到强大的桥梁纽带作用。

关键词： kinase inhibitors   gain of function   oncogenicity   hot spot   molecular modeling   missense mutations  

摘要： Somatic mutations in PIK3CA (phosphatidylinositol-3 kinase, catalytic subunit, alpha isoform) are reported in breast and other human cancers to concentrate at hotspots within its kinase and helical domains. Most of these mutations cause kinase gain of function in vitro and are associated with oncogenicity in vivo. However, little is known about the mechanisms driving tumor development. We have performed computational structural studies on a homology model of wildtype PIK3CA plus recurrent H1047R, H1047L, and P539R mutations, located in the kinase and helical domains, respectively. The time evolution of the structures show that H1047R/L mutants exhibit a larger area of the catalytic cleft between the kinase N- and C-lobes compared with the wildtype that could facilitate the entrance of substrates. This larger area might yield enhanced substrate-to-product turnover associated with oncogenicity. In addition, the H1047R/L mutants display increased kinase activation loop mobility, compared with the wildtype. The P539R mutant forms more hydrogen bonds and salt-bridge interactions than the wildtype, properties that are associated with enhanced thermostability. Mutant-specific differences in the catalytic cleft and activation loop behavior suggest that structure-based mutant-specific inhibitors can be designed for PIK3CA-positive breast cancers.

关键词： 结构振动   自调谐式动力吸振器   振动控制   反馈控制  

摘要： 为了拓宽吸振器的工作带宽,提高吸振器的减振效果,在分析了影响自调谐式动力吸振器减振效果因素的基础上,研制了一种通过调节自身的几何参数来调节固有频率的机械自调谐式动力吸振器,并设计了相应的控制系统。在梁结构实验平台上对该吸振器的动力学特性进行了实验评价,结果表明,该吸振器具有吸振频带宽、减振效果好等优点。

关键词： 柔性机械臂   参数识别   组合结构  

摘要： 将柔性机械臂做成组合结构,利用结合面摩擦效应抑制柔性机械臂的振动。用单根叠层组合柔性臂与实体柔性臂的自由振动对比试验验证组合柔性臂具有优良的抑振性能。用弹簧摩擦副双折线模型和三次非线性弹性力模型建立组合柔性臂的动力学模型。根据组合柔性臂有限元仿真激振试验数据,确定组合柔性臂的形函数和动态恢复力滞迟回线。用动能等效原理、滞迟回线分解法和最小二乘法确定组合柔性臂的动力学模型参数。在Simulink平台上,编制弹簧摩擦副恢复力计算模块,解决含有记忆环节的柔性臂非线性微分方程的数值求解问题。经试验验证,用该模型参数识别方法确定的动力学模型能较准确地反映组合柔性机械臂的动力学性质,为组合柔性机械臂动力学建模、减振性设计提供有效方法。

关键词： synaptosomal associated protein 25   Ternary   SNAP23 gene   SNARE protein  

摘要： Regulated exocytosis is a crucial event for intercellular communication between neurons and astrocytes within the CNS. The soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) complex, composed of synaptobrevin 2, syntaxin and synaptosome-associated protein of 25 kDa or 23 kDa (SNAP25 or SNAP23), is essential in this process. It was reported that SNAP25 and SNAP23 have distinct roles in exocytotic release, where SNAP25, but not SNAP23, supports an exocytotic burst. It is not clear, however, whether this is due to the intrinsic properties of the ternary SNARE complex, containing either SNAP25 or SNAP23, or perhaps due to the differential association of these proteins with ancillary proteins to the complex. Here, using force spectroscopy, we show from single molecule investigations of the SNARE complex, that SNAP23A created a local interaction at the ionic layer by cuffing syntaxin 1A and synaptobrevin 2, similar to the action of SNAP25B;thus either of the ternary complexes would allow positioning of vesicles at a maximal distance of similar to 13 nm from the plasma membrane. However, the stability of the ternary SNARE complex containing SNAP23A is less than half of that for the complex containing SNAP25B. Thus, differences in the stability of the two different ternary complexes could underlie some of the SNAP25/23 differential ability to control the exocytotic burst.