关键词： Computational chemistry   Molecular dynamics   Molecular modelling  

摘要： The first, long time scale (16-ns) ligand field molecular dynamics (LFMD) simulations of the oxy form of tyrosinase are reported. The calculations use our existing type 3 copper force field for the peroxido-bridged [Cu2O2](2+) unit which is here translated from MMFF into the AMBER format together with a new charge scheme. The protein secondary and tertiary structures are not significantly altered by removing the 'caddie' protein, ORF378, which must be bound to tyrosinase before crystals will grow. A comprehensive principal component analysis of the Cartesian coordinates from the final 8 ns shows that the protein backbone is relatively rigid. However, the significant butterfly fold of the [Cu2O2](2+) moiety observed in the X-ray structure, presumably due to the caddie protein tyrosine at the active site, is absent in the simulations. LFMD gives a clear and persistent distinction between equatorial and axial Cu-N distances, with the latter about 0.2 angstrom longer and remaining syn to each other. However, the two coordination spheres display important differences. LFMD simulations of the symmetric model complex [mu-eta(2) :mu(2)-O-2{Cu(MeiM)(3)}(2)](2+) (Meim is 5-methyl-1H-imidazole) provide a mechanism for syn-anti interchange of axial ligands which suggests, in combination with the old experimental X-ray data, the new LFMD simulations and traditional coordination chemistry arguments, that His(54) on Cu-A is 'insipiently axial' and that a combination of a butterfly distortion of the [Cu2O2](2+) group and a rotation of the Cu-A(His)(3) moiety converts the vacant, initially axial, binding site on Cu-A into a much more favourable equatorial site.

关键词： mechanical stimulation   periodontal disease   rat   fibroblasts   collagen   proliferating cell nuclear antigen  

摘要： Background and Objective: Elimination of pathogens is the main aim of periodontal treatment;however, modulation of the host immune response should also be considered. This study aimed to evaluate the effects of mechanical stimulation on periodontal healing in rats. Material and Methods: Before starting the experiment, lipopolysaccharide and proteases were applied once a day, for 4 wk, to both maxillary first molars of 30 rats to induce periodontal disease, and the application was stopped at the end of the 4-wk period. The experiment started immediately following this pretreatment. In the experiment, the left palatal gingiva was stimulated once daily using a powered toothbrush and the right gingiva served as a control (no mechanical stimulation). Pathological changes, and proliferation and cell death in periodontal tissues, were evaluated histometrically and immunohistochemically at baseline (0 wk), and at 1 and 3 wk of stimulation. Results: The control showed a reduction of polymorphonuclear leukocyte infiltration in connective tissue and an increase in the numbers of gingival and periodontal ligament fibroblasts. Mechanical stimulation reduced polymorphonuclear leukocyte infiltration and the area of destroyed collagen in connective tissue, and increased the number of gingival fibroblasts;however, it had no effect on alveolar bone and root resorption or on the number of periodontal ligament fibroblasts. Conclusion: Mechanical stimulation accelerated the healing of gingival inflammation by reducing the infiltration of polymorphonuclear leukocytes and enhancing fibroblast proliferation and collagen synthesis.

关键词： MOLECULAR dynamics   PALLADIUM   INTERFACES (Physical sciences)   METALS   NANOPARTICLES  

摘要： The mechanical properties of extended palladium nanocontacts have been investigated by the molecular dynamics method. The characteristic interatomic distances in the contacts have been determined and the process of the formation of palladium atomic contacts undergoing breaking has been studied for the (100), (110), and (111) orientations of the contact-surface interfaces.

关键词： solutions   QM/MM MD simulation   QMCF MD simulation   hydration structure   germanium ion  

摘要： Structural and dynamical properties of Ge (II) in aqueous solution have been investigated using the novel ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism. The first and second hydration shells were treated by ab initio quantum mechanics at restricted Hartree-Fock (RHF) level using the cc-pVDZ-PP basis set for Ge (II) and Dunning double-zeta plus polarization basis sets for O and H. Besides ligand exchange processes and mean ligand residence times to observe dynamics, tilt- and theta-angle distributions along with an advanced structural parameter, namely radial and angular distribution functions (RAD) for different regions were also evaluated. The combined radial and angular distribution depicted through surface plot and contour map is presented to provide a detailed insight into the density distribution of water molecules around the Ge(2+) ion. A strongly distorted hydration structure with two trigonal pyramidal substructures within the first hydration shell is observed, which demonstrates the lone-pair influence and provides a new basis for the interpretation of the catalytic and pharmacological proper-ties of germanium coordination compounds. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 278-285, 2010

关键词： Plumes (Fluid dynamics)   Diffusion in hydrology   Scientific experimentation   Groundwater tracers   Porous materials   Groundwater pollution  

摘要： Mass transfer, mixing, and therefore reaction rates during transport of solutes in porous media strongly depend on dispersion and diffusion. In particular, transverse mixing is a significant mechanism controlling natural attenuation of contaminant plumes in groundwater. The aim of the present study is to gain a deeper understanding of vertical transverse dispersive mixing of reaction partners in saturated porous media. Multitracer laboratory experiments in a quasi two-dimensional tank filled with glass beads were conducted and transverse dispersion coefficients were determined from high-resolution vertical concentration profiles. We investigated the behavior of conservative tracers (i.e., fluorescein, dissolved oxygen, and bromide), with different aqueous diffusion coefficients, in a range of grain-related Peclet numbers between 1 and 562. The experimental results do not agree with tie classical linear parametric model of hydrodynamic dispersion, in which the transverse component is approximated as the sum of pore diffusion and a compound-independent mechanical dispersion term. The outcome of the multitracer experiments clearly indicates a nonlinear relation between the dispersion coefficient and the average linear velocity. More importantly, we show that transverse mechanical dispersion depends on the diffusion coefficient of the compound, at least at the experimental bench-scale. This result has to be considered in reactive-transport models, because the typical assumption that two reactants with different aqueous diffusive properties are characterized by the same dispersive behavior does not hold anymore.

关键词： Thermal explosion   Ignition   Mechanical activation   Time-resolved X-ray diffraction   Phase transformation  

摘要： Time-resolved X-ray diffraction (TRXRD) techniques, which allowed for in-situ investigation of the dynamics of phase transformation during rapid, gasless heterogeneous reactions, were used to study the thermal explosion (TE) process in the stoichiometric Ni-Al system. Comparison of the phase transformation sequences for initial mixtures of the precursors and those after short-term high-energy ball milling shows that while for the former case the necessary condition for TE is melting of the reactive media, in the latter case TE occurs solely through solid-state reactions. It is also concluded that the rates of solid-state reaction are significantly enhanced due to an increase of oxygen-free contact surface area and a decrease of the scale of heterogeneity in the composite particles formed during mechanical treatment. (C) 2009 Elsevier B.V. All rights reserved.

关键词： DNA/chemistry   DNA/metabolism   DNA Polymerase I/chemistry   DNA Polymerase I/metabolism   DNA Replication   Molecular Dynamics Simulation   Substrate Specificity  

摘要： In this issue of Structure, Golosov et al. present molecular dynamics simulations that illuminate the process of DNA translocation by an A-family DNA polymerase. Several distinct phases are identified that have not been visualized through crystallographic studies.

摘要： We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our combined quantum-mechanical/molecular-mechanical approach demonstrates that molecular-mechanical force fields are able to describe both the backbone and base-base interactions within the highly distorted nucleic acid structures produced by stretching the DNA from the 5' ends, which include conformations containing disassociated basepairs, just as well as these force fields describe relaxed DNA conformations. The molecular-dynamics simulations indicate that the force-induced melting pathway is sequence-dependent and is influenced by the availability of noncanonical hydrogen-bond interactions that can assist the disassociation of the DNA basepairs. The biological implications of these results are discussed.

关键词： CHEMICAL kinetics   LIQUORS   OXIDATION   MECHANICAL pulping process   RADICALS (Chemistry)   SODIUM compounds   CARBOXYLIC acids  

摘要： The kinetics and reuse of spent liquor in the TEMPO-mediated oxidation of mechanical pulp have been Studied. It was found that the oxidation reaction of the mechanical Pulp by the 2,2,6,6-tetramethyl piperidine-1-oxyl radical (TEMPO)-NaBr-NaOCl system can be approximately described by first-order kinetics with respect to TEMPO and NaBr. In the concentration range used, the rate constant k is directly proportional to the concentration of TEMPO and NaBr, whereas the concentration of NaOCl determines the end of conversion of the primary alcohol groups Oil the mechanical pulp into carboxylic acid groups. It was also found that the spent reaction liquor call be recycled and reused with reinforced addition of NaOCl without additional TEMPO and NaBr and remains effective in generating carboxylic acid groups Oil mechanical pulp.

关键词： 惯量伪速度   动力学建模   递推   高效率  

摘要： 对于多个体组成的复杂大型多体系统,传统动力学建模方法推导过程费时费力,通过形位参数建立的二阶微分方程组冗长、繁多并且计算量大难以求解。伪速度从运动的本质出发,引入速度级独立变量代替广义坐标,拓宽了独立变量的选取范围,得到了形式简洁的可积分的一阶微分方程组。笔者通过旋量递推与惯量伪速度结合,研究了高效率的建模方法,对两类伪速度进行区分,并阐述了惯量伪速度的物理含义,并得到了伪速度建模的优点。得到的对角化一阶动力学方程形式简洁,直接面向计算机编程实现,易于设计解耦控制或非交互控制,并把建模过程应用于Puma560机器人中。